4LFC | pdb_00004lfc

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb4LFC/pdb
• NAKB: 4LFC

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8
• Mutation(s): No 


• Deposited: 2013-06-26 Released: 2014-07-02 
• Deposition Author(s): Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 788.39 kDa 
• Atom Count: 51,888 
• Modeled Residue Count: 3,910 
• Deposited Residue Count: 4,063 
• Unique protein chains: 20
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S2	B	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371  Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S3	C	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372  Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S4	D	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373  Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S5	E	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5  Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S6	F	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S7	G	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S8	H	138	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S9	I	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374  Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S10	J	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7  Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S11	K	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376  Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S12	L	135	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for F6DEQ7 (Thermus thermophilus (strain SG0.5JP17-16)) Explore F6DEQ7  Go to UniProtKB:  F6DEQ7

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S13	M	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377  Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S14	N	61	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S15	O	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76  Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S16	P	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3  Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S17	Q	105	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S18	R	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0  Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S19	S	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S20	T	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380  Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein THX	U	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A	1,522	Thermus thermophilus HB8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TOY	CF [auth A]	TOBRAMYCIN C18 H37 N5 O9 NLVFBUXFDBBNBW-PBSUHMDJSA-N
ZN	EF [auth D], MF [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	AE [auth A], BE [auth A], CE [auth A], DE [auth A], EE [auth A], FE [auth A], QD [auth A], RD [auth A], SD [auth A], TD [auth A], UD [auth A], VD [auth A], WD [auth A], XD [auth A], YD [auth A], ZD [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	AA [auth A], AB [auth A], AC [auth A], AD [auth A], AF [auth A], BA [auth A], BB [auth A], BC [auth A], BD [auth A], BF [auth A], CA [auth A], CB [auth A], CC [auth A], CD [auth A], DA [auth A], DB [auth A], DC [auth A], DD [auth A], DF [auth B], EA [auth A], EB [auth A], EC [auth A], ED [auth A], FA [auth A], FB [auth A], FC [auth A], FD [auth A], FF [auth D], GA [auth A], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth D], HA [auth A], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth E], IA [auth A], IB [auth A], IC [auth A], ID [auth A], IE [auth A], IF [auth H], JA [auth A], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth J], KA [auth A], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth K], LA [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth M], MA [auth A], MB [auth A], MC [auth A], MD [auth A], ME [auth A], NA [auth A], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NF [auth N], OA [auth A], OB [auth A], OC [auth A], OD [auth A], OE [auth A], OF [auth N], PA [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], PF [auth Q], QA [auth A], QB [auth A], QC [auth A], QE [auth A], QF [auth S], RA [auth A], RB [auth A], RC [auth A], RE [auth A], SA [auth A], SB [auth A], SC [auth A], SE [auth A], TA [auth A], TB [auth A], TC [auth A], TE [auth A], UA [auth A], UB [auth A], UC [auth A], UE [auth A], V [auth A], VA [auth A], VB [auth A], VC [auth A], VE [auth A], W [auth A], WA [auth A], WB [auth A], WC [auth A], WE [auth A], X [auth A], XA [auth A], XB [auth A], XC [auth A], XE [auth A], Y [auth A], YA [auth A], YB [auth A], YC [auth A], YE [auth A], Z [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZE [auth A]	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: 3.60 Å
• R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 401.831	α = 90
b = 401.831	β = 90
c = 175.888	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2025-02-19
  Changes: Data collection, Database references, Derived calculations, Structure summary