Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 51888 
• Residue Count: 3910 
• Unique protein chains: 20
• Unique nucleic acid chains: 1

4LFC

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

• DOI: 10.2210/pdb4LFC/pdb
• NDB: NA2536

• 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 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

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

To be published.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S2	B	256	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rpsB, rps2, TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsC, rps3, TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsD, rps4, TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsE, TTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsF, TTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsG, rps7, TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsH, TTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore P0DOY9  Go to UniProtKB:  P0DOY9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S9	I	128	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rpsI, rps9, TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsJ, TTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsK, rps11, TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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
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  Gene Names: rpsM, rps13, TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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
Find proteins for A0A0N0BLP2 (Thermus aquaticus) Explore A0A0N0BLP2  Go to UniProtKB:  A0A0N0BLP2

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S15	O	89	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rpsO, TTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsP, TTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsQ, TTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore P0DOY7  Go to UniProtKB:  P0DOY7

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein S18	R	88	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rpsR, TTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsS, TTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsT, rps20, TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) 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  Gene Names: rpsU, TTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A	1522	Thermus thermophilus HB8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TOY	A	TOBRAMYCIN C18 H37 N5 O9 NLVFBUXFDBBNBW-PBSUHMDJSA-N
ZN	D, N	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	A, B, D, E, H, J, K, M, N, Q, S	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 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• 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

• Deposited Date: 2013-06-26 
• 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