4KVB

Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17

• PDB DOI: https://doi.org/10.2210/pdb4KVB/pdb
• NAKB: 4KVB

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB27
• Mutation(s): No 


• Deposited: 2013-05-22 Released: 2014-06-04 
• Deposition Author(s): Murphy, E.L., Jogl, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Structural robustness of the ribosome inferred from the X-ray crystal structure of a 30S ribosomal subunit lacking ribosomal protein S17

Connetti, J.L., Murphy, E.L., Dahlberg, A.E., Gregory, S.T., Jogl, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 19-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 776.9 kDa 
• Atom Count: 51,128 
• Modelled Residue Count: 3,807 
• Deposited Residue Count: 3,957 
• Unique protein chains: 19
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B	256	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62662 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62662  Go to UniProtKB:  P62662

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C	239	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62663 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62663  Go to UniProtKB:  P62663

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D	209	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62664 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62664  Go to UniProtKB:  P62664

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E	162	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62665 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62665  Go to UniProtKB:  P62665

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F	101	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62666 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62666  Go to UniProtKB:  P62666

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G	156	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62667 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62667  Go to UniProtKB:  P62667

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	H	138	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62668 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62668  Go to UniProtKB:  P62668

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I	128	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62669 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62669  Go to UniProtKB:  P62669

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J	105	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62653 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62653  Go to UniProtKB:  P62653

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K	129	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62654 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62654  Go to UniProtKB:  P62654

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L	134	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P61941 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P61941  Go to UniProtKB:  P61941

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M	126	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62655 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62655  Go to UniProtKB:  P62655

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	N	61	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62656 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62656  Go to UniProtKB:  P62656

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O	89	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62657 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62657  Go to UniProtKB:  P62657

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P	88	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62238 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62238  Go to UniProtKB:  P62238

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	Q [auth R]	88	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62659 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62659  Go to UniProtKB:  P62659

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	R [auth S]	93	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62660 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62660  Go to UniProtKB:  P62660

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	S [auth T]	106	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62661 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62661  Go to UniProtKB:  P62661

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	T [auth U]	27	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62613 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62613  Go to UniProtKB:  P62613

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A	1,522	Thermus thermophilus HB27

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AH [auth D], FH [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	AG [auth A], BG [auth A], CG [auth A], DG [auth A], EG [auth A], FG [auth A], GG [auth A], HG [auth A], IG [auth A], JG [auth A], KG [auth A], LG [auth A], MG [auth A], NG [auth A], OG [auth A], PF [auth A], PG [auth A], QF [auth A], QG [auth A], RF [auth A], RG [auth A], SF [auth A], SG [auth A], TF [auth A], TG [auth A], UF [auth A], UG [auth A], VF [auth A], VG [auth A], WF [auth A], WG [auth A], XF [auth A], XG [auth A], YF [auth A], ZF [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	AA [auth A], AB [auth A], AC [auth A], AD [auth A], AE [auth A], AF [auth A], BA [auth A], BB [auth A], BC [auth A], BD [auth A], BE [auth A], BF [auth A], BH [auth D], CA [auth A], CB [auth A], CC [auth A], CD [auth A], CE [auth A], CF [auth A], CH [auth E], DA [auth A], DB [auth A], DC [auth A], DD [auth A], DE [auth A], DF [auth A], DH [auth E], EA [auth A], EB [auth A], EC [auth A], ED [auth A], EE [auth A], EF [auth A], EH [auth M], FA [auth A], FB [auth A], FC [auth A], FD [auth A], FE [auth A], FF [auth A], GA [auth A], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth A], GH [auth U], HA [auth A], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth A], IA [auth A], IB [auth A], IC [auth A], ID [auth A], IE [auth A], IF [auth A], JA [auth A], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth A], KA [auth A], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth A], LA [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth A], MA [auth A], MB [auth A], MC [auth A], MD [auth A], ME [auth A], MF [auth A], NA [auth A], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NF [auth A], OA [auth A], OB [auth A], OC [auth A], OD [auth A], OE [auth A], OF [auth A], PA [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], QA [auth A], QB [auth A], QC [auth A], QD [auth A], QE [auth A], RA [auth A], RB [auth A], RC [auth A], RD [auth A], RE [auth A], SA [auth A], SB [auth A], SC [auth A], SD [auth A], SE [auth A], TA [auth A], TB [auth A], TC [auth A], TD [auth A], TE [auth A], U [auth A], UA [auth A], UB [auth A], UC [auth A], UD [auth A], UE [auth A], V [auth A], VA [auth A], VB [auth A], VC [auth A], VD [auth A], VE [auth A], W [auth A], WA [auth A], WB [auth A], WC [auth A], WD [auth A], WE [auth A], X [auth A], XA [auth A], XB [auth A], XC [auth A], XD [auth A], XE [auth A], Y [auth A], YA [auth A], YB [auth A], YC [auth A], YD [auth A], YE [auth A], YG [auth A], Z [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth A], ZE [auth A], ZG [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0TD	L	L-PEPTIDE LINKING	C5 H9 N O4 S		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 397.316	α = 90
b = 397.316	β = 90
c = 215.505	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Murphy, E.L., Jogl, G.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2025-02-19
  Changes: Data collection, Structure summary