Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.
To be published.
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 
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 
wwPDB Validation   3D Report Full Report

Literature
Macromolecules
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(by identity cutoff)  |  Structure
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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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Entity ID: 11 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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Entity ID: 15 | |||||
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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 | |||||
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Entity ID: 16 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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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 | |||||
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Find similar nucleic acids by: 
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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 | 3D Interactions | |
TOY Query on TOY | A | TOBRAMYCIN C18 H37 N5 O9 NLVFBUXFDBBNBW-PBSUHMDJSA-N | Ligand Interaction | ||
ZN Query on ZN | D, N | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | Ligand Interaction | ||
K Query on K | A | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | Ligand Interaction | ||
MG Query on MG | A, B, D, E, H, J, K, M, N, Q, S | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | Ligand Interaction |
Modified Residues  1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
0TD Query on 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 Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
PHENIX | phasing |
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.