5JVG Ribosome date May 11, 2016
title The Large Ribosomal Subunit From Deinococcus Radiodurans In With Avilamycin
authors M.Krupkin, I.Wekselman, D.Matzov, Z.Eyal, Y.Diskin Posner, H.Roze E.Zimmerman, A.Bashan, A.Yonath
compound source
Molecule: 23s Ribosomal Rna
Chain: X
 Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 5s Ribosomal Rna
Chain: Y
Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L2
Chain: A
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L3
Chain: B
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L4
Chain: C
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L5
Chain: D
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L6
Chain: E
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L11
Chain: F
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L13
Chain: G
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L14
Chain: H
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L15
Chain: I
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L16
Chain: J
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L17
Chain: K
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L18
Chain: L
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L19
Chain: M
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L20
Chain: N
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L21
Chain: O
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L22
Chain: P
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L23
Chain: Q
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L24
Chain: R
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L27
Chain: T
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L28
Chain: U
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L29
Chain: V
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L30
Chain: W
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L32
Chain: Z
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L33
Chain: 1
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L34
Chain: 2
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L35
Chain: 3
Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422
symmetry Space Group: I 2 2 2
R_factor 0.211 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
170.034 412.632 698.142 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.43 Å
ligand 6NO, MG, MPD, SPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


Z


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3677 Kb) [Save to disk]
  • Biological Unit Coordinates (5jvg.pdb1.gz) 3624 Kb
  • LPC: Ligand-Protein Contacts for 5JVG
  • CSU: Contacts of Structural Units for 5JVG
  • Structure Factors (3659 Kb)
  • Retrieve 5JVG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JVG from S2C, [Save to disk]
  • Re-refined 5jvg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JVG in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5JVG
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jvg_Y] [5jvg_M] [5jvg_B] [5jvg_I] [5jvg_F] [5jvg_X] [5jvg_1] [5jvg_N] [5jvg_A] [5jvg_Z] [5jvg_H] [5jvg_D] [5jvg_W] [5jvg_P] [5jvg_G] [5jvg_K] [5jvg_E] [5jvg_J] [5jvg_T] [5jvg_2] [5jvg_R] [5jvg_S] [5jvg] [5jvg_Q] [5jvg_V] [5jvg_U] [5jvg_L] [5jvg_C] [5jvg_O] [5jvg_3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JVG: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
    • Other resources with information on 5JVG
  • Community annotation for 5JVG at PDBWiki (http://pdbwiki.org)

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