4DV1

Crystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, U20G, bound with streptomycin

Structural Biology Knowledgebase: 4DV1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.150

Literature

Macromolecules
Sequence Display for 4DV1

Classification: RIBOSOME / ANTIBIOTIC

Total Structure Weight: 790693.94


Macromolecule Entities
Molecule Chains Length Organism Details
ribosomal protein S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S5 E 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S6 F 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S7 G 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S8 H 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S9 I 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S10 J 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S12 L 135 Thermus thermophilus Gene Name(s): rpsL TTHA1697
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S14 N 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S15 O 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S16 P 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S17 Q 105 Thermus thermophilus Mutation: E96Q
Gene Name(s): rpsQ TTHA1683
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S18 R 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S19 S 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein S20 T 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ribosomal protein THX U 27 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B, D, E, H, I, J, K, M, N, P, S, T MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
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: 3.85 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.150
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 403.45 α = 90.00
b = 403.45 β = 90.00
c = 173.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-22
  • Released Date: 2013-02-27
  • Deposition author(s): Demirci, H., Murphy IV, F., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.

Revision History

No revisions since initial release