1QVG

Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui

Structural Biology Knowledgebase: 1QVG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1QVG

Classification: RIBOSOME

Total Structure Weight: 1460820.25


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2P A 239 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
50S ribosomal protein L3P B 337 Haloarcula marismortui Mutation: ΔP310, F310R
Gene Name(s): rpl3 rrnAC1611
50S ribosomal protein L4E C 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
50S ribosomal protein L5P D 176 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
50S ribosomal protein L6P E 177 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
50S ribosomal protein L7Ae F 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
50S RIBOSOMAL PROTEIN L10E G 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
L10 Ribosomal Protein H 167 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
50S ribosomal protein L13P I 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
50S ribosomal protein L14P J 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
50S ribosomal protein L15P K 164 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
L15 Ribosomal Protein L 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
50S ribosomal protein L18P M 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
50S ribosomal protein L18e N 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
50S ribosomal protein L19E O 148 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
50S ribosomal protein L21e P 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
50S ribosomal protein L22P Q 154 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
50S ribosomal protein L23P R 84 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
50S ribosomal protein L24P S 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
50S ribosomal protein L24E T 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
50S ribosomal protein L29P U 70 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
50S ribosomal protein L30P V 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
50S ribosomal protein L31e W 91 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
50S ribosomal protein L32E X 240 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
L37Ae 50S ribosomal protein Y 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
50S ribosomal protein L37e Z 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
50S ribosomal protein L39e 1 48 Haloarcula marismortui Mutation: ΔR31
Gene Name(s): rpl39e rrnAC3112
50S ribosomal protein L44E 2 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Macromolecule Entities
Molecule Chains Length Organism Details
23S ribosomal rna 0 2922 Haloarcula marismortui
5S ribosomal RNA 9 122 Haloarcula marismortui
Oligonucleotide CCA 3, 4, 5 3 synthetic

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CD
Query on CD

2, N, T, Y, Z CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

0, 2, A, B, I, J, K, L, M, N, Q, X CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

0, 2, 9, A, B, J, S, X MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

0, 9, A, C, H, I, K, L, P, Q, R SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.201
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 213.52 α = 90.00
b = 300.61 β = 90.00
c = 573.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-08-27
  • Released Date: 2003-11-11
  • Deposition author(s): Schmeing, T.M., Moore, P.B., Steitz, T.A.

Revision History

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