6OTR

Dimeric E.coli YoeB bound to Thermus thermophilus 70S post-cleavage (AAU)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.

Pavelich, I.J., Maehigashi, T., Hoffer, E.D., Ruangprasert, A., Miles, S.J., Dunham, C.M.

(2019) Nucleic Acids Res 47: 10400-10413

  • DOI: https://doi.org/10.1093/nar/gkz760
  • Primary Citation of Related Structures:  
    6NY6, 6OTR, 6OXA, 6OXI

  • PubMed Abstract: 

    Chromosomally-encoded toxin-antitoxin complexes are ubiquitous in bacteria and regulate growth through the release of the toxin component typically in a stress-dependent manner. Type II ribosome-dependent toxins adopt a RelE-family RNase fold and inhibit translation by degrading mRNAs while bound to the ribosome. Here, we present biochemical and structural studies of the Escherichia coli YoeB toxin interacting with both a UAA stop and an AAU sense codon in pre- and post-mRNA cleavage states to provide insights into possible mRNA substrate selection. Both mRNAs undergo minimal changes during the cleavage event in contrast to type II ribosome-dependent RelE toxin. Further, the 16S rRNA decoding site nucleotides that monitor the mRNA in the aminoacyl(A) site adopt different orientations depending upon which toxin is present. Although YoeB is a RelE family member, it is the sole ribosome-dependent toxin that is dimeric. We show that engineered monomeric YoeB is active against mRNAs bound to both the small and large subunit. However, the stability of monomeric YoeB is reduced ∼20°C, consistent with potential YoeB activation during heat shock in E. coli as previously demonstrated. These data provide a molecular basis for the ability of YoeB to function in response to thermal stress.

    • Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth QB],
GB [auth XB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth QC],
HB [auth XC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth QD],
IB [auth XD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth QE],
JB [auth XE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth QF],
KB [auth XF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth QG],
LB [auth XG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth QH],
MB [auth XH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth QI],
NB [auth XI]		128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth QJ],
OB [auth XJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth QK],
PB [auth XK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth QL],
QB [auth XL]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth QM],
RB [auth XM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth QN],
SB [auth XN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth QO],
TB [auth XO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth QP],
UB [auth XP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth QQ],
VB [auth XQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth QR],
WB [auth XR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth QS],
XB [auth XS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth QT],
YB [auth XT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth QU],
ZB [auth XU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Addiction module toxin, Txe/YoeB familyDC [auth XY],
EC [auth XZ],
Y [auth QY],
Z [auth QZ]		84Escherichia coliMutation(s): 0 
EC: 3.1
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Find proteins for J7QFC0 (Escherichia coli)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AA [auth R0],
FC [auth Y0]		85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BA [auth R1],
GC [auth Y1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CA [auth R2],
HC [auth Y2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth R3],
IC [auth Y3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31EA [auth R4],
JC [auth Y4]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32FA [auth R5],
KC [auth Y5]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33GA [auth R6],
LC [auth Y6]		54Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34HA [auth R7],
MC [auth Y7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35IA [auth R8],
NC [auth Y8]		65Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36JA [auth R9],
OC [auth Y9]		37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2MA [auth RD],
RC [auth YD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3NA [auth RE],
SC [auth YE]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4OA [auth RF],
TC [auth YF]		210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PA [auth RG],
UC [auth YG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6QA [auth RH],
VC [auth YH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9RA [auth RI],
WC [auth YI]		148Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13SA [auth RN],
XC [auth YN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14TA [auth RO],
YC [auth YO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15UA [auth RP],
ZC [auth YP]		150Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16AD [auth YQ],
VA [auth RQ]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17BD [auth YR],
WA [auth RR]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18CD [auth YS],
XA [auth RS]		112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19DD [auth YT],
YA [auth RT]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20ED [auth YU],
ZA [auth RU]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21AB [auth RV],
FD [auth YV]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22BB [auth RW],
GD [auth YW]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23CB [auth RX],
HD [auth YX]		96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24DB [auth RY],
ID [auth YY]		110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25EB [auth RZ],
JD [auth YZ]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth QA],
FB [auth XA]		1,521Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
tRNA-fMetAC [auth XV],
BC [auth XW],
V [auth QV],
W [auth QW]		77Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
mRNACC [auth XX],
X [auth QX]		20Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
23S rRNAKA [auth RA],
PC [auth YA]		2,915Thermus thermophilus HB8
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Entity ID: 36
MoleculeChains LengthOrganismImage
5S rRNALA [auth RB],
QC [auth YB]		124Thermus thermophilus HB8
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Entity ID: 56
MoleculeChains LengthOrganismImage
CCPuroKD [auth ZA],
LD [auth ZB]		3synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P
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BH [auth QX],
XX		ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
SF4
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NX [auth XD],
VG [auth QD]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN
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FH [auth R6],
GH [auth R9],
SX [auth XN],
XG [auth QN],
ZX [auth Y6]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
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AAA [auth YA]
ABA [auth YA]
ACA [auth YA]
ADA [auth YA]
AE [auth QA]
AAA [auth YA],
ABA [auth YA],
ACA [auth YA],
ADA [auth YA],
AE [auth QA],
AEA [auth YA],
AF [auth QA],
AFA [auth YA],
AG [auth QA],
AGA [auth YA],
AH [auth QV],
AHA [auth YA],
AI [auth RA],
AIA [auth YA],
AJ [auth RA],
AJA [auth YA],
AK [auth RA],
AKA [auth YA],
AL [auth RA],
ALA [auth YE],
AM [auth RA],
AN [auth RA],
AO [auth RA],
AP [auth RA],
AQ [auth RA],
AR [auth RA],
AS [auth RA],
AT [auth RB],
AU [auth XA],
AV [auth XA],
AW [auth XA],
AX [auth XA],
AY [auth Y9],
AZ [auth YA],
BAA [auth YA],
BBA [auth YA],
BCA [auth YA],
BDA [auth YA],
BE [auth QA],
BEA [auth YA],
BF [auth QA],
BFA [auth YA],
BG [auth QA],
BGA [auth YA],
BHA [auth YA],
BI [auth RA],
BIA [auth YA],
BJ [auth RA],
BJA [auth YA],
BK [auth RA],
BKA [auth YA],
BL [auth RA],
BLA [auth YE],
BM [auth RA],
BN [auth RA],
BO [auth RA],
BP [auth RA],
BQ [auth RA],
BR [auth RA],
BS [auth RA],
BT [auth RB],
BU [auth XA],
BV [auth XA],
BW [auth XA],
BX [auth XA],
BY [auth YA],
BZ [auth YA],
CAA [auth YA],
CBA [auth YA],
CCA [auth YA],
CDA [auth YA],
CE [auth QA],
CEA [auth YA],
CF [auth QA],
CFA [auth YA],
CG [auth QA],
CGA [auth YA],
CH [auth R0],
CHA [auth YA],
CI [auth RA],
CIA [auth YA],
CJ [auth RA],
CJA [auth YA],
CK [auth RA],
CKA [auth YA],
CL [auth RA],
CLA [auth YE],
CM [auth RA],
CN [auth RA],
CO [auth RA],
CP [auth RA],
CQ [auth RA],
CR [auth RA],
CS [auth RA],
CT [auth RB],
CU [auth XA],
CV [auth XA],
CW [auth XA],
CX [auth XA],
CY [auth YA],
CZ [auth YA],
DAA [auth YA],
DBA [auth YA],
DCA [auth YA],
DDA [auth YA],
DE [auth QA],
DEA [auth YA],
DF [auth QA],
DFA [auth YA],
DG [auth QA],
DGA [auth YA],
DH [auth R0],
DHA [auth YA],
DI [auth RA],
DIA [auth YA],
DJ [auth RA],
DJA [auth YA],
DK [auth RA],
DKA [auth YA],
DL [auth RA],
DLA [auth YE],
DM [auth RA],
DN [auth RA],
DO [auth RA],
DP [auth RA],
DQ [auth RA],
DR [auth RA],
DS [auth RA],
DT [auth RD],
DU [auth XA],
DV [auth XA],
DW [auth XA],
DX [auth XA],
DY [auth YA],
DZ [auth YA],
EAA [auth YA],
EBA [auth YA],
ECA [auth YA],
EDA [auth YA],
EE [auth QA],
EEA [auth YA],
EF [auth QA],
EFA [auth YA],
EG [auth QA],
EGA [auth YA],
EH [auth R5],
EHA [auth YA],
EI [auth RA],
EIA [auth YA],
EJ [auth RA],
EJA [auth YA],
EK [auth RA],
EKA [auth YA],
EL [auth RA],
ELA [auth YG],
EM [auth RA],
EN [auth RA],
EO [auth RA],
EP [auth RA],
EQ [auth RA],
ER [auth RA],
ES [auth RA],
ET [auth RE],
EU [auth XA],
EV [auth XA],
EW [auth XA],
EX [auth XA],
EY [auth YA],
EZ [auth YA],
FAA [auth YA],
FBA [auth YA],
FCA [auth YA],
FDA [auth YA],
FE [auth QA],
FEA [auth YA],
FF [auth QA],
FFA [auth YA],
FG [auth QA],
FGA [auth YA],
FHA [auth YA],
FI [auth RA],
FIA [auth YA],
FJ [auth RA],
FJA [auth YA],
FK [auth RA],
FKA [auth YA],
FL [auth RA],
FLA [auth YO],
FM [auth RA],
FN [auth RA],
FO [auth RA],
FP [auth RA],
FQ [auth RA],
FR [auth RA],
FS [auth RA],
FT [auth RE],
FU [auth XA],
FV [auth XA],
FW [auth XA],
FX [auth XA],
FY [auth YA],
FZ [auth YA],
GAA [auth YA],
GBA [auth YA],
GCA [auth YA],
GDA [auth YA],
GE [auth QA],
GEA [auth YA],
GF [auth QA],
GFA [auth YA],
GG [auth QA],
GGA [auth YA],
GHA [auth YA],
GI [auth RA],
GIA [auth YA],
GJ [auth RA],
GJA [auth YA],
GK [auth RA],
GKA [auth YA],
GL [auth RA],
GLA [auth YP],
GM [auth RA],
GN [auth RA],
GO [auth RA],
GP [auth RA],
GQ [auth RA],
GR [auth RA],
GS [auth RA],
GT [auth RN],
GU [auth XA],
GV [auth XA],
GW [auth XA],
GX [auth XA],
GY [auth YA],
GZ [auth YA],
HAA [auth YA],
HBA [auth YA],
HCA [auth YA],
HDA [auth YA],
HE [auth QA],
HEA [auth YA],
HF [auth QA],
HFA [auth YA],
HG [auth QA],
HGA [auth YA],
HH [auth RA],
HHA [auth YA],
HI [auth RA],
HIA [auth YA],
HJ [auth RA],
HJA [auth YA],
HK [auth RA],
HKA [auth YA],
HL [auth RA],
HLA [auth YQ],
HM [auth RA],
HN [auth RA],
HO [auth RA],
HP [auth RA],
HQ [auth RA],
HR [auth RA],
HS [auth RA],
HT [auth RO],
HU [auth XA],
HV [auth XA],
HW [auth XA],
HX [auth XA],
HY [auth YA],
HZ [auth YA],
IAA [auth YA],
IBA [auth YA],
ICA [auth YA],
IDA [auth YA],
IE [auth QA],
IEA [auth YA],
IF [auth QA],
IFA [auth YA],
IG [auth QA],
IGA [auth YA],
IH [auth RA],
IHA [auth YA],
II [auth RA],
IIA [auth YA],
IJ [auth RA],
IJA [auth YA],
IK [auth RA],
IKA [auth YA],
IL [auth RA],
ILA [auth YR],
IM [auth RA],
IN [auth RA],
IO [auth RA],
IP [auth RA],
IQ [auth RA],
IR [auth RA],
IS [auth RA],
IT [auth RP],
IU [auth XA],
IV [auth XA],
IW [auth XA],
IX [auth XA],
IY [auth YA],
IZ [auth YA],
JAA [auth YA],
JBA [auth YA],
JCA [auth YA],
JDA [auth YA],
JE [auth QA],
JEA [auth YA],
JF [auth QA],
JFA [auth YA],
JG [auth QA],
JGA [auth YA],
JH [auth RA],
JHA [auth YA],
JI [auth RA],
JIA [auth YA],
JJ [auth RA],
JJA [auth YA],
JK [auth RA],
JKA [auth YA],
JL [auth RA],
JLA [auth YS],
JM [auth RA],
JN [auth RA],
JO [auth RA],
JP [auth RA],
JQ [auth RA],
JR [auth RA],
JS [auth RA],
JT [auth RQ],
JU [auth XA],
JV [auth XA],
JW [auth XA],
JX [auth XA],
JY [auth YA],
JZ [auth YA],
KAA [auth YA],
KBA [auth YA],
KCA [auth YA],
KDA [auth YA],
KE [auth QA],
KEA [auth YA],
KF [auth QA],
KFA [auth YA],
KG [auth QA],
KGA [auth YA],
KH [auth RA],
KHA [auth YA],
KI [auth RA],
KIA [auth YA],
KJ [auth RA],
KJA [auth YA],
KK [auth RA],
KKA [auth YA],
KL [auth RA],
KLA [auth YV],
KM [auth RA],
KN [auth RA],
KO [auth RA],
KP [auth RA],
KQ [auth RA],
KR [auth RA],
KS [auth RA],
KT [auth RR],
KU [auth XA],
KV [auth XA],
KW [auth XA],
KX [auth XA],
KY [auth YA],
KZ [auth YA],
LAA [auth YA],
LBA [auth YA],
LCA [auth YA],
LDA [auth YA],
LE [auth QA],
LEA [auth YA],
LF [auth QA],
LFA [auth YA],
LG [auth QA],
LGA [auth YA],
LH [auth RA],
LHA [auth YA],
LI [auth RA],
LIA [auth YA],
LJ [auth RA],
LJA [auth YA],
LK [auth RA],
LKA [auth YA],
LL [auth RA],
LM [auth RA],
LN [auth RA],
LO [auth RA],
LP [auth RA],
LQ [auth RA],
LR [auth RA],
LS [auth RA],
LT [auth XA],
LU [auth XA],
LV [auth XA],
LW [auth XA],
LX [auth XA],
LY [auth YA],
LZ [auth YA],
MAA [auth YA],
MBA [auth YA],
MCA [auth YA],
MD [auth QA],
MDA [auth YA],
ME [auth QA],
MEA [auth YA],
MF [auth QA],
MFA [auth YA],
MG [auth QA],
MGA [auth YA],
MH [auth RA],
MHA [auth YA],
MI [auth RA],
MIA [auth YA],
MJ [auth RA],
MJA [auth YA],
MK [auth RA],
MKA [auth YA],
ML [auth RA],
MM [auth RA],
MN [auth RA],
MO [auth RA],
MP [auth RA],
MQ [auth RA],
MR [auth RA],
MS [auth RA],
MT [auth XA],
MU [auth XA],
MV [auth XA],
MW [auth XA],
MX [auth XA],
MY [auth YA],
MZ [auth YA],
NAA [auth YA],
NBA [auth YA],
NCA [auth YA],
ND [auth QA],
NDA [auth YA],
NE [auth QA],
NEA [auth YA],
NF [auth QA],
NFA [auth YA],
NG [auth QA],
NGA [auth YA],
NH [auth RA],
NHA [auth YA],
NI [auth RA],
NIA [auth YA],
NJ [auth RA],
NJA [auth YA],
NK [auth RA],
NKA [auth YA],
NL [auth RA],
NM [auth RA],
NN [auth RA],
NO [auth RA],
NP [auth RA],
NQ [auth RA],
NR [auth RA],
NS [auth RA],
NT [auth XA],
NU [auth XA],
NV [auth XA],
NW [auth XA],
NY [auth YA],
NZ [auth YA],
OAA [auth YA],
OBA [auth YA],
OCA [auth YA],
OD [auth QA],
ODA [auth YA],
OE [auth QA],
OEA [auth YA],
OF [auth QA],
OFA [auth YA],
OG [auth QA],
OGA [auth YA],
OH [auth RA],
OHA [auth YA],
OI [auth RA],
OIA [auth YA],
OJ [auth RA],
OJA [auth YA],
OK [auth RA],
OKA [auth YA],
OL [auth RA],
OM [auth RA],
ON [auth RA],
OO [auth RA],
OP [auth RA],
OQ [auth RA],
OR [auth RA],
OS [auth RA],
OT [auth XA],
OU [auth XA],
OV [auth XA],
OW [auth XA],
OX [auth XD],
OY [auth YA],
OZ [auth YA],
PAA [auth YA],
PBA [auth YA],
PCA [auth YA],
PD [auth QA],
PDA [auth YA],
PE [auth QA],
PEA [auth YA],
PF [auth QA],
PFA [auth YA],
PG [auth QA],
PGA [auth YA],
PH [auth RA],
PHA [auth YA],
PI [auth RA],
PIA [auth YA],
PJ [auth RA],
PJA [auth YA],
PK [auth RA],
PKA [auth YA],
PL [auth RA],
PM [auth RA],
PN [auth RA],
PO [auth RA],
PP [auth RA],
PQ [auth RA],
PR [auth RA],
PS [auth RA],
PT [auth XA],
PU [auth XA],
PV [auth XA],
PW [auth XA],
PX [auth XE],
PY [auth YA],
PZ [auth YA],
QAA [auth YA],
QBA [auth YA],
QCA [auth YA],
QD [auth QA],
QDA [auth YA],
QE [auth QA],
QEA [auth YA],
QF [auth QA],
QFA [auth YA],
QG [auth QA],
QGA [auth YA],
QH [auth RA],
QHA [auth YA],
QI [auth RA],
QIA [auth YA],
QJ [auth RA],
QJA [auth YA],
QK [auth RA],
QKA [auth YA],
QL [auth RA],
QM [auth RA],
QN [auth RA],
QO [auth RA],
QP [auth RA],
QQ [auth RA],
QR [auth RA],
QS [auth RA],
QT [auth XA],
QU [auth XA],
QV [auth XA],
QW [auth XA],
QX [auth XF],
QY [auth YA],
QZ [auth YA],
RAA [auth YA],
RBA [auth YA],
RCA [auth YA],
RD [auth QA],
RDA [auth YA],
RE [auth QA],
REA [auth YA],
RF [auth QA],
RFA [auth YA],
RG [auth QA],
RGA [auth YA],
RH [auth RA],
RHA [auth YA],
RI [auth RA],
RIA [auth YA],
RJ [auth RA],
RJA [auth YA],
RK [auth RA],
RKA [auth YA],
RL [auth RA],
RM [auth RA],
RN [auth RA],
RO [auth RA],
RP [auth RA],
RQ [auth RA],
RR [auth RA],
RS [auth RA],
RT [auth XA],
RU [auth XA],
RV [auth XA],
RW [auth XA],
RX [auth XL],
RY [auth YA],
RZ [auth YA],
SAA [auth YA],
SBA [auth YA],
SCA [auth YA],
SD [auth QA],
SDA [auth YA],
SE [auth QA],
SEA [auth YA],
SF [auth QA],
SFA [auth YA],
SG [auth QA],
SGA [auth YA],
SH [auth RA],
SHA [auth YA],
SI [auth RA],
SIA [auth YA],
SJ [auth RA],
SJA [auth YA],
SK [auth RA],
SKA [auth YB],
SL [auth RA],
SM [auth RA],
SN [auth RA],
SO [auth RA],
SP [auth RA],
SQ [auth RA],
SR [auth RA],
SS [auth RA],
ST [auth XA],
SU [auth XA],
SV [auth XA],
SW [auth XA],
SY [auth YA],
SZ [auth YA],
TAA [auth YA],
TBA [auth YA],
TCA [auth YA],
TD [auth QA],
TDA [auth YA],
TE [auth QA],
TEA [auth YA],
TF [auth QA],
TFA [auth YA],
TG [auth QA],
TGA [auth YA],
TH [auth RA],
THA [auth YA],
TI [auth RA],
TIA [auth YA],
TJ [auth RA],
TJA [auth YA],
TK [auth RA],
TKA [auth YB],
TL [auth RA],
TM [auth RA],
TN [auth RA],
TO [auth RA],
TP [auth RA],
TQ [auth RA],
TR [auth RA],
TS [auth RA],
TT [auth XA],
TU [auth XA],
TV [auth XA],
TW [auth XA],
TX [auth XV],
TY [auth YA],
TZ [auth YA],
UAA [auth YA],
UBA [auth YA],
UCA [auth YA],
UD [auth QA],
UDA [auth YA],
UE [auth QA],
UEA [auth YA],
UF [auth QA],
UFA [auth YA],
UG [auth QA],
UGA [auth YA],
UH [auth RA],
UHA [auth YA],
UI [auth RA],
UIA [auth YA],
UJ [auth RA],
UJA [auth YA],
UK [auth RA],
UKA [auth YB],
UL [auth RA],
UM [auth RA],
UN [auth RA],
UO [auth RA],
UP [auth RA],
UQ [auth RA],
UR [auth RA],
US [auth RA],
UT [auth XA],
UU [auth XA],
UV [auth XA],
UW [auth XA],
UX [auth XV],
UY [auth YA],
UZ [auth YA],
VAA [auth YA],
VBA [auth YA],
VCA [auth YA],
VD [auth QA],
VDA [auth YA],
VE [auth QA],
VEA [auth YA],
VF [auth QA],
VFA [auth YA],
VGA [auth YA],
VH [auth RA],
VHA [auth YA],
VI [auth RA],
VIA [auth YA],
VJ [auth RA],
VJA [auth YA],
VK [auth RA],
VKA [auth YB],
VL [auth RA],
VM [auth RA],
VN [auth RA],
VO [auth RA],
VP [auth RA],
VQ [auth RA],
VR [auth RA],
VS [auth RA],
VT [auth XA],
VU [auth XA],
VV [auth XA],
VW [auth XA],
VX [auth XV],
VY [auth YA],
VZ [auth YA],
WAA [auth YA],
WBA [auth YA],
WCA [auth YA],
WD [auth QA],
WDA [auth YA],
WE [auth QA],
WEA [auth YA],
WF [auth QA],
WFA [auth YA],
WG [auth QE],
WGA [auth YA],
WH [auth RA],
WHA [auth YA],
WI [auth RA],
WIA [auth YA],
WJ [auth RA],
WJA [auth YA],
WK [auth RA],
WKA [auth YB],
WL [auth RA],
WM [auth RA],
WN [auth RA],
WO [auth RA],
WP [auth RA],
WQ [auth RA],
WR [auth RA],
WS [auth RA],
WT [auth XA],
WU [auth XA],
WV [auth XA],
WW [auth XA],
WX [auth XV],
WY [auth YA],
WZ [auth YA],
XAA [auth YA],
XBA [auth YA],
XCA [auth YA],
XD [auth QA],
XDA [auth YA],
XE [auth QA],
XEA [auth YA],
XF [auth QA],
XFA [auth YA],
XGA [auth YA],
XH [auth RA],
XHA [auth YA],
XI [auth RA],
XIA [auth YA],
XJ [auth RA],
XJA [auth YA],
XK [auth RA],
XKA [auth YB],
XL [auth RA],
XM [auth RA],
XN [auth RA],
XO [auth RA],
XP [auth RA],
XQ [auth RA],
XR [auth RA],
XS [auth RA],
XT [auth XA],
XU [auth XA],
XV [auth XA],
XW [auth XA],
XY [auth YA],
XZ [auth YA],
YAA [auth YA],
YBA [auth YA],
YCA [auth YA],
YD [auth QA],
YDA [auth YA],
YE [auth QA],
YEA [auth YA],
YF [auth QA],
YFA [auth YA],
YG [auth QV],
YGA [auth YA],
YH [auth RA],
YHA [auth YA],
YI [auth RA],
YIA [auth YA],
YJ [auth RA],
YJA [auth YA],
YK [auth RA],
YKA [auth YD],
YL [auth RA],
YM [auth RA],
YN [auth RA],
YO [auth RA],
YP [auth RA],
YQ [auth RA],
YR [auth RA],
YS [auth RA],
YT [auth XA],
YU [auth XA],
YV [auth XA],
YW [auth XA],
YX [auth Y5],
YY [auth YA],
YZ [auth YA],
ZAA [auth YA],
ZBA [auth YA],
ZCA [auth YA],
ZD [auth QA],
ZDA [auth YA],
ZE [auth QA],
ZEA [auth YA],
ZF [auth QA],
ZFA [auth YA],
ZG [auth QV],
ZGA [auth YA],
ZH [auth RA],
ZHA [auth YA],
ZI [auth RA],
ZIA [auth YA],
ZJ [auth RA],
ZJA [auth YA],
ZK [auth RA],
ZKA [auth YD],
ZL [auth RA],
ZM [auth RA],
ZN [auth RA],
ZO [auth RA],
ZP [auth RA],
ZQ [auth RA],
ZR [auth RA],
ZS [auth RA],
ZT [auth XA],
ZU [auth XA],
ZV [auth XA],
ZW [auth XA],
ZY [auth YA],
ZZ [auth YA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.364α = 90
b = 451.705β = 90
c = 607.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB 0953714
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM093278

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description