5DM6 Ribosome date Sep 08, 2015
title Crystal Structure Of The 50s Ribosomal Subunit From Deinococ Radiodurans
authors T.Kaminishi, A.Schedlbauer, B.Ochoa-Lizarralde, S.R.Connell, P.F
compound source
Molecule: 50s Ribosomal Protein L1
Chain
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L2
Chain: A

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L3
Chain: B

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L4
Chain: C

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L5
Chain: D

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L6
Chain: E

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L11
Chain: F

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L13
Chain: G

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L14
Chain: H

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L15
Chain: I

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L16
Chain: J

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L17
Chain: K

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L18
Chain: L

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L19
Chain: M

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L20
Chain: N

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L21
Chain: O

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L22
Chain: P

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L23
Chain: Q

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L24
Chain: R

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L27
Chain: T

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L28
Chain: U

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L29
Chain: V

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L30
Chain: W

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L32
Chain: Z

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L35
Chain: 3

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 23s Ribosomal Rna
Chain: X

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 5s Ribosomal Rna
Chain: Y

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
symmetry Space Group: I 2 2 2
R_factor 0.235 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.900 410.760 696.120 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
0


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


Primary referenceCrystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A., Kaminishi T, Schedlbauer A, Fabbretti A, Brandi L, Ochoa-Lizarralde B, He CG, Milon P, Connell SR, Gualerzi CO, Fucini P, Nucleic Acids Res. 2015 Nov 16;43(20):10015-25. doi: 10.1093/nar/gkv975. Epub, 2015 Oct 12. PMID:26464437
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1781 Kb) [Save to disk]
  • Biological Unit Coordinates (5dm6.pdb1.gz) 1766 Kb
  • LPC: Ligand-Protein Contacts for 5DM6
  • CSU: Contacts of Structural Units for 5DM6
  • Structure Factors (5094 Kb)
  • Retrieve 5DM6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DM6 from S2C, [Save to disk]
  • Re-refined 5dm6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DM6 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 5DM6
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5dm6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dm6_3] [5dm6_R] [5dm6_S] [5dm6_H] [5dm6_E] [5dm6_W] [5dm6_C] [5dm6_I] [5dm6_O] [5dm6_K] [5dm6_A] [5dm6_Z] [5dm6_0] [5dm6_T] [5dm6_P] [5dm6_B] [5dm6_N] [5dm6_X] [5dm6_Y] [5dm6] [5dm6_F] [5dm6_J] [5dm6_M] [5dm6_2] [5dm6_G] [5dm6_Q] [5dm6_V] [5dm6_1] [5dm6_U] [5dm6_L] [5dm6_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DM6: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 5DM6
  • Community annotation for 5DM6 at PDBWiki (http://pdbwiki.org)

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