4JI1

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Structural Biology Knowledgebase: 4JI1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.165

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JI1

Classification: Ribosome / Antibiotic

Total Structure Weight: 792567.90


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 Mutation: P94L
Gene Name(s): rpsL TTHA1697
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 EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S rRNA A 1522 Thermus thermophilus

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

A STREPTOMYCIN
STREPTOMYCIN A (Synonym)
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

D, N ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, D, E, F, H, I, J, K, N, P, Q, S, T MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (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: 3.14 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.165
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 403.17 α = 90.00
b = 403.17 β = 90.00
c = 173.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-05
  • Released Date: 2013-11-06
  • Deposition author(s): Demirci, H., Wang, L., Murphy IV, F., Murphy, E., Carr, J., Blanchard, S., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Revision History

  • 2013-12-04
    Type: Citation | Details: Citation update