4V8I

Crystal structure of YfiA bound to the 70S ribosome.

• PDB DOI: https://doi.org/10.2210/pdb4V8I/pdb
• Entry: 4V8I supersedes: 3V2C, 3V2D, 3V2E, 3V2F
• NAKB: 4V8I

• Classification: Ribosome/Inhibitor
• Organism(s): Thermus thermophilus, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-12 Released: 2014-07-09 
• Deposition Author(s): Polikanov, Y.S., Blaha, G.M., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.

Polikanov, Y.S., Blaha, G.M., Steitz, T.A.

(2012) Science 336: 915-918

• PubMed: 22605777 
• DOI: https://doi.org/10.1126/science.1218538
• Primary Citation of Related Structures:  
  4V8G, 4V8H, 4V8I


• PubMed Abstract: 
  

  Eubacteria inactivate their ribosomes as 100S dimers or 70S monomers upon entry into stationary phase. In Escherichia coli, 100S dimer formation is mediated by ribosome modulation factor (RMF) and hibernation promoting factor (HPF), or alternatively, the YfiA protein inactivates ribosomes as 70S monomers. Here, we present high-resolution crystal structures of the Thermus thermophilus 70S ribosome in complex with each of these stationary-phase factors. The binding site of RMF overlaps with that of the messenger RNA (mRNA) Shine-Dalgarno sequence, which prevents the interaction between the mRNA and the 16S ribosomal RNA. The nearly identical binding sites of HPF and YfiA overlap with those of the mRNA, transfer RNA, and initiation factors, which prevents translation initiation. The binding of RMF and HPF, but not YfiA, to the ribosome induces a conformational change of the 30S head domain that promotes 100S dimer formation.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4,412.53 kDa 
• Atom Count: 287,173 
• Modelled Residue Count: 20,617 
• Deposited Residue Count: 21,484 
• Unique protein chains: 50
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S2	B [auth AB], CB	256	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S3	C [auth AC], DB [auth CC]	239	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S4	D [auth AD], EB [auth CD]	209	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S5	E [auth AE], FB [auth CE]	162	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S6	F [auth AF], GB [auth CF]	101	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S7	G [auth AG], HB [auth CG]	156	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S8	H [auth AH], IB [auth CH]	138	Thermus thermophilus	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S9	I [auth AI], JB [auth CI]	128	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S10	J [auth AJ], KB [auth CJ]	105	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S11	K [auth AK], LB [auth CK]	129	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S12	L [auth AL], MB [auth CL]	132	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S13	M [auth AM], NB [auth CM]	126	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S14	N [auth AN], OB [auth CN]	61	Thermus thermophilus	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S15	O [auth AO], PB [auth CO]	89	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S16	P [auth AP], QB [auth CP]	88	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S17	Q [auth AQ], RB [auth CQ]	105	Thermus thermophilus	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S18	R [auth AR], SB [auth CR]	88	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S19	S [auth AS], TB [auth CS]	93	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein S20	T [auth AT], UB [auth CT]	106	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal Protein THX	U [auth AU], VB [auth CU]	27	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SIH3

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-associated inhibitor A	V [auth AY], WB [auth CY]	119	Escherichia coli K-12	Mutation(s): 0  Gene Names: b2597, JW2578, raiA, yfiA
UniProt
Find proteins for P0AD49 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AD49

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L2	Y [auth BD], ZB [auth DD]	276	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60405

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L3	AC [auth DE], Z [auth BE]	206	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN8

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L4	AA [auth BF], BC [auth DF]	210	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN9

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L5	BA [auth BG], CC [auth DG]	182	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ0

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L6	CA [auth BH], DC [auth DH]	180	Thermus thermophilus	Mutation(s): 0

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L9	DA [auth BI], EC [auth DI]	148	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SLQ1

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L13	EA [auth BN], FC [auth DN]	140	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60488

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L14	FA [auth BO], GC [auth DO]	122	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP8

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L15	GA [auth BP], HC [auth DP]	150	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ7

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L16	HA [auth BQ], IC [auth DQ]	141	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60489

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L17	IA [auth BR], JC [auth DR]	118	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q9Z9H5

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L18	JA [auth BS], KC [auth DS]	112	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ4

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L19	KA [auth BT], LC [auth DT]	146	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60490

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L20	LA [auth BU], MC [auth DU]	118	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60491

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L21	MA [auth BV], NC [auth DV]	101	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60492

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L22	NA [auth BW], OC [auth DW]	113	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP3

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L23	OA [auth BX], PC [auth DX]	96	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP0

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L24	PA [auth BY], QC [auth DY]	110	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q56435 (Thermus thermophilus) Go to UniProtKB:  Q56435

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L25	QA [auth BZ], RC [auth DZ]	206	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHZ1

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L27	RA [auth B0], SC [auth D0]	85	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60493

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L28	SA [auth B1], TC [auth D1]	98	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60494

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L29	TA [auth B2], UC [auth D2]	72	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP6

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L30	UA [auth B3], VC [auth D3]	60	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ6

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L31	VA [auth B4], WC [auth D4]	71	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SJE1

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L32	WA [auth B5], XC [auth D5]	60	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80339

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L33	XA [auth B6], YC [auth D6]	54	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P35871

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L34	YA [auth B7], ZC [auth D7]	49	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80340

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S Ribosomal Protein L35	AD [auth D8], ZA [auth B8]	65	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SKU1

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	AB [auth B9], BD [auth D9]	37	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80256 (Thermus thermophilus) Go to UniProtKB:  P80256

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S Ribosomal RNA	A [auth AA], BB [auth CA]	1,522	Thermus thermophilus

Entity ID: 23
Molecule	Chains	Length	Organism	Image
23S Ribosomal RNA	W [auth BA], XB [auth DA]	2,915	Thermus thermophilus

Entity ID: 24
Molecule	Chains	Length	Organism	Image
5S Ribosomal RNA	X [auth BB], YB [auth DB]	122	Thermus thermophilus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	ARA [auth B4], CRA [auth B5], DRA [auth B6], GZA [auth CD], HRA [auth B9], IZA [auth CN], JZB [auth DY], LL [auth AD], MQA [auth BY], MZB [auth D4], NZB [auth D5], QZB [auth D6], UL [auth AN], VZB [auth D9]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth BA], AAB [auth DA], ABA [auth BA], ABB [auth DA], ACA [auth BA], ACB [auth DA], ADA [auth BA], ADB [auth DA], AE [auth AA], AEA [auth BA], AEB [auth DA], AF [auth AA], AFA [auth BA], AFB [auth DA], AG [auth AA], AGA [auth BA], AGB [auth DA], AH [auth AA], AHA [auth BA], AHB [auth DA], AI [auth AA], AIA [auth BA], AIB [auth DA], AJ [auth AA], AJA [auth BA], AJB [auth DA], AK [auth AA], AKA [auth BA], AKB [auth DA], AL [auth AA], ALA [auth BA], ALB [auth DA], AM [auth BA], AMA [auth BA], AMB [auth DA], AN [auth BA], ANA [auth BA], ANB [auth DA], AO [auth BA], AOA [auth BB], AOB [auth DA], AP [auth BA], APA [auth BE], APB [auth DA], AQ [auth BA], AQA [auth BS], AQB [auth DA], AR [auth BA], ARB [auth DA], AS [auth BA], ASA [auth CA], ASB [auth DA], AT [auth BA], ATA [auth CA], ATB [auth DA], AU [auth BA], AUA [auth CA], AUB [auth DA], AV [auth BA], AVA [auth CA], AVB [auth DA], AW [auth BA], AWA [auth CA], AWB [auth DA], AX [auth BA], AXA [auth CA], AXB [auth DA], AY [auth BA], AYA [auth CA], AYB [auth DB], AZ [auth BA], AZA [auth CA], AZB [auth DQ], BAA [auth BA], BAB [auth DA], BBA [auth BA], BBB [auth DA], BCA [auth BA], BCB [auth DA], BDA [auth BA], BDB [auth DA], BE [auth AA], BEA [auth BA], BEB [auth DA], BF [auth AA], BFA [auth BA], BFB [auth DA], BG [auth AA], BGA [auth BA], BGB [auth DA], BH [auth AA], BHA [auth BA], BHB [auth DA], BI [auth AA], BIA [auth BA], BIB [auth DA], BJ [auth AA], BJA [auth BA], BJB [auth DA], BK [auth AA], BKA [auth BA], BKB [auth DA], BL [auth AA], BLA [auth BA], BLB [auth DA], BM [auth BA], BMA [auth BA], BMB [auth DA], BN [auth BA], BNA [auth BA], BNB [auth DA], BO [auth BA], BOA [auth BB], BOB [auth DA], BP [auth BA], BPA [auth BE], BPB [auth DA], BQ [auth BA], BQA [auth BT], BQB [auth DA], BR [auth BA], BRA [auth B5], BRB [auth DA], BS [auth BA], BSA [auth CA], BSB [auth DA], BT [auth BA], BTA [auth CA], BTB [auth DA], BU [auth BA], BUA [auth CA], BUB [auth DA], BV [auth BA], BVA [auth CA], BVB [auth DA], BW [auth BA], BWA [auth CA], BWB [auth DA], BX [auth BA], BXA [auth CA], BXB [auth DA], BY [auth BA], BYA [auth CA], BYB [auth DB], BZ [auth BA], BZA [auth CA], BZB [auth DQ], CAA [auth BA], CAB [auth DA], CBA [auth BA], CBB [auth DA], CCA [auth BA], CCB [auth DA], CD [auth AA], CDA [auth BA], CDB [auth DA], CE [auth AA], CEA [auth BA], CEB [auth DA], CF [auth AA], CFA [auth BA], CFB [auth DA], CG [auth AA], CGA [auth BA], CGB [auth DA], CH [auth AA], CHA [auth BA], CHB [auth DA], CI [auth AA], CIA [auth BA], CIB [auth DA], CJ [auth AA], CJA [auth BA], CJB [auth DA], CK [auth AA], CKA [auth BA], CKB [auth DA], CL [auth AA], CLA [auth BA], CLB [auth DA], CM [auth BA], CMA [auth BA], CMB [auth DA], CN [auth BA], CNA [auth BA], CNB [auth DA], CO [auth BA], COA [auth BB], COB [auth DA], CP [auth BA], CPA [auth BE], CPB [auth DA], CQ [auth BA], CQA [auth BT], CQB [auth DA], CR [auth BA], CRB [auth DA], CS [auth BA], CSA [auth CA], CSB [auth DA], CT [auth BA], CTA [auth CA], CTB [auth DA], CU [auth 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BA], TGB [auth DA], TH [auth AA], THA [auth BA], THB [auth DA], TI [auth AA], TIA [auth BA], TIB [auth DA], TJ [auth AA], TJA [auth BA], TJB [auth DA], TK [auth AA], TKA [auth BA], TKB [auth DA], TL [auth AM], TLA [auth BA], TLB [auth DA], TM [auth BA], TMA [auth BA], TMB [auth DA], TN [auth BA], TNA [auth BA], TNB [auth DA], TO [auth BA], TOA [auth BD], TOB [auth DA], TP [auth BA], TPA [auth BQ], TPB [auth DA], TQ [auth BA], TQA [auth B0], TQB [auth DA], TR [auth BA], TRA [auth CA], TRB [auth DA], TS [auth BA], TSA [auth CA], TSB [auth DA], TT [auth BA], TTA [auth CA], TTB [auth DA], TU [auth BA], TUA [auth CA], TUB [auth DA], TV [auth BA], TVA [auth CA], TVB [auth DA], TW [auth BA], TWA [auth CA], TWB [auth DA], TX [auth BA], TXA [auth CA], TXB [auth DA], TY [auth BA], TYA [auth CA], TYB [auth DF], TZ [auth BA], TZA [auth DA], TZB [auth D8], UAA [auth BA], UAB [auth DA], UBA [auth BA], UBB [auth DA], UCA [auth BA], UCB [auth DA], UD [auth AA], UDA [auth BA], UDB [auth DA], UE [auth AA], UEA [auth BA], UEB [auth DA], UF [auth AA], UFA [auth BA], UFB [auth DA], UG [auth AA], UGA [auth BA], UGB [auth DA], UH [auth AA], UHA [auth BA], UHB [auth DA], UI [auth AA], UIA [auth BA], UIB [auth DA], UJ [auth AA], UJA [auth BA], UJB [auth DA], UK [auth AA], UKA [auth BA], UKB [auth DA], ULA [auth BA], ULB [auth DA], UM [auth BA], UMA [auth BA], UMB [auth DA], UN [auth BA], UNA [auth BA], UNB [auth DA], UO [auth BA], UOA [auth BD], UOB [auth DA], UP [auth BA], UPA [auth BQ], UPB [auth DA], UQ [auth BA], UQA [auth B1], UQB [auth DA], UR [auth BA], URA [auth CA], URB [auth DA], US [auth BA], USA [auth CA], USB [auth DA], UT [auth BA], UTA [auth CA], UTB [auth DA], UU [auth BA], UUA [auth CA], UUB [auth DA], UV [auth BA], UVA [auth CA], UVB [auth DA], UW [auth BA], UWA [auth CA], UWB [auth DA], UX [auth BA], UXA [auth CA], UXB [auth DA], UY [auth BA], UYA [auth CA], UYB [auth DO], UZ [auth BA], UZA [auth DA], UZB [auth D8], VAA [auth BA], VAB [auth DA], VBA [auth BA], VBB [auth DA], VCA [auth BA], VCB [auth DA], VD [auth AA], VDA [auth BA], VDB [auth DA], VE [auth AA], VEA [auth BA], VEB [auth DA], VF [auth AA], VFA [auth BA], VFB [auth DA], VG [auth AA], VGA [auth BA], VGB [auth DA], VH [auth AA], VHA [auth BA], VHB [auth DA], VI [auth AA], VIA [auth BA], VIB [auth DA], VJ [auth AA], VJA [auth BA], VJB [auth DA], VK [auth AA], VKA [auth BA], VKB [auth DA], VL [auth AP], VLA [auth BA], VLB [auth DA], VM [auth BA], VMA [auth BA], VMB [auth DA], VN [auth BA], VNA [auth BA], VNB [auth DA], VO [auth BA], VOA [auth BD], VOB [auth DA], VP [auth BA], VPA [auth BR], VPB [auth DA], VQ [auth BA], VQA [auth B2], VQB [auth DA], VR [auth BA], VRA [auth CA], VRB [auth DA], VS [auth BA], VSA [auth CA], VSB [auth DA], VT [auth BA], VTA [auth CA], VTB [auth DA], VU [auth BA], VUA [auth CA], VUB [auth DA], VV [auth BA], VVA [auth CA], VVB [auth DA], VW [auth BA], VWA [auth CA], VWB [auth DA], VX [auth BA], VXA [auth CA], VXB [auth DA], VY [auth BA], VYA [auth CA], VYB [auth DO], VZ [auth BA], VZA [auth DA], WAA [auth BA], WAB [auth DA], WBA [auth BA], WBB [auth DA], WCA [auth BA], WCB [auth DA], WD [auth AA], WDA [auth BA], WDB [auth DA], WE [auth AA], WEA [auth BA], WEB [auth DA], WF [auth AA], WFA [auth BA], WFB [auth DA], WG [auth AA], WGA [auth BA], WGB [auth DA], WH [auth AA], WHA [auth BA], WHB [auth DA], WI [auth AA], WIA [auth BA], WIB [auth DA], WJ [auth AA], WJA [auth BA], WJB [auth DA], WK [auth AA], WKA [auth BA], WKB [auth DA], WL [auth BA], WLA [auth BA], WLB [auth DA], WM [auth BA], WMA [auth BA], WMB [auth DA], WN [auth BA], WNA [auth BA], WNB [auth DA], WO [auth BA], WOA [auth BD], WOB [auth DA], WP [auth BA], WPA [auth BR], WPB [auth DA], WQ [auth BA], WQA [auth B2], WQB [auth DA], WR [auth BA], WRA [auth CA], WRB [auth DA], WS [auth BA], WSA [auth CA], WSB [auth DA], WT [auth BA], WTA [auth CA], WTB [auth DA], WU [auth BA], WUA [auth CA], WUB [auth DA], WV [auth BA], WVA [auth CA], WVB [auth DA], WW [auth BA], WWA [auth CA], WWB [auth DA], WX [auth BA], WXA [auth CA], WXB [auth DA], WY [auth BA], WYA [auth CA], WYB [auth DO], WZ [auth BA], WZA [auth DA], WZB [auth D9], XAA [auth BA], XAB [auth DA], XBA [auth BA], XBB [auth DA], XCA [auth BA], XCB [auth DA], XD [auth AA], XDA [auth BA], XDB [auth DA], XE [auth AA], XEA [auth BA], XEB [auth DA], XF [auth AA], XFA [auth BA], XFB [auth DA], XG [auth AA], XGA [auth BA], XGB [auth DA], XH [auth AA], XHA [auth BA], XHB [auth DA], XI [auth AA], XIA [auth BA], XIB [auth DA], XJ [auth AA], XJA [auth BA], XJB [auth DA], XK [auth AA], XKA [auth BA], XKB [auth DA], XL [auth BA], XLA [auth BA], XLB [auth DA], XM [auth BA], XMA [auth BA], XMB [auth DA], XN [auth BA], XNA [auth BB], XNB [auth DA], XO [auth BA], XOA [auth BE], XOB [auth DA], XP [auth BA], XPA [auth BR], XPB [auth DA], XQ [auth BA], XQA [auth B3], XQB [auth DA], XR [auth BA], XRA [auth CA], XRB [auth DA], XS [auth BA], XSA [auth CA], XSB [auth DA], XT [auth BA], XTA [auth CA], XTB [auth DA], XU [auth BA], XUA [auth CA], XUB [auth DA], XV [auth BA], XVA [auth CA], XVB [auth DA], XW [auth BA], XWA [auth CA], XWB [auth DA], XX [auth BA], XXA [auth CA], XXB [auth DB], XY [auth BA], XYA [auth CA], XYB [auth DP], XZ [auth BA], XZA [auth DA], YAA [auth BA], YAB [auth DA], YBA [auth BA], YBB [auth DA], YCA [auth BA], YCB [auth DA], YD [auth AA], YDA [auth BA], YDB [auth DA], YE [auth AA], YEA [auth BA], YEB [auth DA], YF [auth AA], YFA [auth BA], YFB [auth DA], YG [auth AA], YGA [auth BA], YGB [auth DA], YH [auth AA], YHA [auth BA], YHB [auth DA], YI [auth AA], YIA [auth BA], YIB [auth DA], YJ [auth AA], YJA [auth BA], YJB [auth DA], YK [auth AA], YKA [auth BA], YKB [auth DA], YL [auth BA], YLA [auth BA], YLB [auth DA], YM [auth BA], YMA [auth BA], YMB [auth DA], YN [auth BA], YNA [auth BB], YNB [auth DA], YO [auth BA], YOA [auth BE], YOB [auth DA], YP [auth BA], YPA [auth BR], YPB [auth DA], YQ [auth BA], YQA [auth B3], YQB [auth DA], YR [auth BA], YRA [auth CA], YRB [auth DA], YS [auth BA], YSA [auth CA], YSB [auth DA], YT [auth BA], YTA [auth CA], YTB [auth DA], YU [auth BA], YUA [auth CA], YUB [auth DA], YV [auth BA], YVA [auth CA], YVB [auth DA], YW [auth BA], YWA [auth CA], YWB [auth DA], YX [auth BA], YXA [auth CA], YXB [auth DB], YY [auth BA], YYA [auth CA], YYB [auth DP], YZ [auth BA], YZA [auth DA], ZAA [auth BA], ZAB [auth DA], ZBA [auth BA], ZBB [auth DA], ZCA [auth BA], ZCB [auth DA], ZD [auth AA], ZDA [auth BA], ZDB [auth DA], ZE [auth AA], ZEA [auth BA], ZEB [auth DA], ZF [auth AA], ZFA [auth BA], ZFB [auth DA], ZG [auth AA], ZGA [auth BA], ZGB [auth DA], ZH [auth AA], ZHA [auth BA], ZHB [auth DA], ZI [auth AA], ZIA [auth BA], ZIB [auth DA], ZJ [auth AA], ZJA [auth BA], ZJB [auth DA], ZK [auth AA], ZKA [auth BA], ZKB [auth DA], ZL [auth BA], ZLA [auth BA], ZLB [auth DA], ZM [auth BA], ZMA [auth BA], ZMB [auth DA], ZN [auth BA], ZNA [auth BB], ZNB [auth DA], ZO [auth BA], ZOA [auth BE], ZOB [auth DA], ZP [auth BA], ZPA [auth BR], ZPB [auth DA], ZQ [auth BA], ZQA [auth B3], ZQB [auth DA], ZR [auth BA], ZRA [auth CA], ZRB [auth DA], ZS [auth BA], ZSA [auth CA], ZSB [auth DA], ZT [auth BA], ZTA [auth CA], ZTB [auth DA], ZU [auth BA], ZUA [auth CA], ZUB [auth DA], ZV [auth BA], ZVA [auth CA], ZVB [auth DA], ZW [auth BA], ZWA [auth CA], ZWB [auth DA], ZX [auth BA], ZXA [auth CA], ZXB [auth DB], ZY [auth BA], ZYA [auth CA], ZYB [auth DP], ZZ [auth BA], ZZA [auth DA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.63	α = 90
b = 449.3	β = 90
c = 620.9	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
PHENIX	model building
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Polikanov, Y.S., Blaha, G.M., Steitz, T.A.
• This entry supersedes: 3V2C, 3V2D, 3V2E, 3V2F

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary