2VQF

MODIFIED URIDINES WITH C5-METHYLENE SUBSTITUENTS AT THE FIRST POSITION OF THE TRNA ANTICODON STABILIZE U-G WOBBLE PAIRING DURING DECODING

Structural Biology Knowledgebase: 2VQF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.223

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VQF

Classification: RIBOSOME

Total Structure Weight: 799921.85


Macromolecule Entities
Molecule Chains Length Organism Details
30S RIBOSOMAL PROTEIN S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
30S RIBOSOMAL PROTEIN S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
30S RIBOSOMAL PROTEIN S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
30S RIBOSOMAL PROTEIN S5 E 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
30S RIBOSOMAL PROTEIN S6 F 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
30S RIBOSOMAL PROTEIN S7 G 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
30S RIBOSOMAL PROTEIN S8 H 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
30S RIBOSOMAL PROTEIN S9 I 128 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
30S RIBOSOMAL PROTEIN S10 J 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
30S RIBOSOMAL PROTEIN S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
30S RIBOSOMAL PROTEIN S12 L 135 Thermus thermophilus Gene Name(s): rpsL TTHA1697
30S RIBOSOMAL PROTEIN S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
30S RIBOSOMAL PROTEIN S14 TYPE Z N 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
30S RIBOSOMAL PROTEIN S15 O 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
30S RIBOSOMAL PROTEIN S16 P 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
30S RIBOSOMAL PROTEIN S17 Q 105 Thermus thermophilus Gene Name(s): rpsQ rps17
30S RIBOSOMAL PROTEIN S18 R 88 Thermus thermophilus Gene Name(s): rpsR rps18
30S RIBOSOMAL PROTEIN S19 S 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
30S RIBOSOMAL PROTEIN S20 T 106 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
30S 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 CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY
5'-R(*UP*UP*GP*AP*AP*AP)-3' X 6 Thermus thermophilus
5'-R(*GP*CP*AP*UP*GP*CP*U*TM2P*AP*AP*AP *AP*CP*AP*UP*GP*C)-3' Y 17 Thermus thermophilus

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

Z PAROMOMYCIN
CATENULIN,, AMMINOSIDIN (Synonym)
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

Z ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

Z POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TM2
Query on TM2
Y non-polymer C12 H20 N3 O12 P S --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.223
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 402.48 α = 90.00
b = 402.48 β = 90.00
c = 175.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-14
  • Released Date: 2008-04-29
  • Deposition author(s): Kurata, S., Weixlbaumer, A., Ohtsuki, T., Shimazaki, T., Wada, T., Kirino, Y., Takai, K., Watanabe, K., Ramakrishnan, V., Suzuki, T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4