4LFC

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Structural Biology Knowledgebase: 4LFC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.163

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4LFC

Classification: ribosome

Total Structure Weight: 788396.85


Macromolecule Entities
Molecule Chains Length Organism Details
ribosomal protein S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
ribosomal protein S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
ribosomal protein S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
ribosomal protein S5 E 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
ribosomal protein S6 F 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
ribosomal protein S7 G 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
ribosomal protein S8 H 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
ribosomal protein S9 I 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
ribosomal protein S10 J 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
ribosomal protein S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
ribosomal protein S12 L 135 Thermus thermophilus
ribosomal protein S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
ribosomal protein S14 N 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
ribosomal protein S15 O 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
ribosomal protein S16 P 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
ribosomal protein S17 Q 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
ribosomal protein S18 R 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
ribosomal protein S19 S 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
ribosomal protein S20 T 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
ribosomal protein THX U 27 Thermus thermophilus Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S rRNA A 1522 Thermus thermophilus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A, B, D, E, H, J, K, M, N, Q, S MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
TOY
Query on TOY

A TOBRAMYCIN
4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL- 5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY- CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO- PYRAN-3,5-DIOL (Synonym)
C18 H37 N5 O9
NLVFBUXFDBBNBW-PBSUHMDJSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

D, N ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 9 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
A RNA LINKING C9 H13 N2 O9 P U
7MG
Query on 7MG
A RNA LINKING C11 H18 N5 O8 P G
M2G
Query on M2G
A RNA LINKING C12 H18 N5 O8 P G
5MC
Query on 5MC
A RNA LINKING C10 H16 N3 O8 P C
2MG
Query on 2MG
A RNA LINKING C11 H16 N5 O8 P G
4OC
Query on 4OC
A RNA LINKING C11 H18 N3 O8 P C
UR3
Query on UR3
A RNA LINKING C10 H15 N2 O9 P U
MA6
Query on MA6
A RNA LINKING C12 H18 N5 O7 P A
0TD
Query on 0TD
L L-PEPTIDE LINKING C5 H9 N O4 S ASP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.163
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 401.83 α = 90.00
b = 401.83 β = 90.00
c = 175.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

No revisions since initial release