4WF9 Ribosome date Sep 14, 2014
title The Crystal Structure Of The Large Ribosomal Subunit Of Stap Aureus In Complex With Telithromycin
authors Z.Eyal, D.Matzov, M.Krupkin, I.Wekselman, E.Zimmerman, H.Rozenber A.Bashan, A.E.Yonath
compound source
Molecule: 23s Ribosomal Rna
Chain: X
 Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 5s Ribosomal Rna
Chain: Y
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L2
Chain: A
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L3
Chain: B
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L4
Chain: C
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L5
Chain: D
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L6
Chain: E
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L13
Chain: G
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L14
Chain: H
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L15
Chain: I
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L16
Chain: J
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L17
Chain: K
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L18
Chain: L
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L19
Chain: M
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L20
Chain: N
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L21
Chain: O
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L22
Chain: P
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L23
Chain: Q
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L24
Chain: R
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc
Organism_scientific: Staphylococcus Aureus (Strain Usa300)
Organism_taxid: 367830
Strain: Usa300

Molecule: 50s Ribosomal Protein L27
Chain: T
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L29
Chain: V
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L30
Chain: W
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L32
Chain: Z
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L34
Chain: 2
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L35
Chain: 3
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325
symmetry Space Group: P 65 2 2
R_factor 0.192 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
282.660 282.660 877.075 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.43 Å
ligand EOH, EPE, MG, MN, MPD, SPD, TEL enzyme
Gene
Ontology
ChainFunctionProcessComponent
2


3


A


B


C


D


E


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


W


Z


Primary referenceStructural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus., Eyal Z, Matzov D, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A, Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):E5805-14. doi:, 10.1073/pnas.1517952112. Epub 2015 Oct 13. PMID:26464510
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3347 Kb) [Save to disk]
  • Biological Unit Coordinates (4wf9.pdb1.gz) 3318 Kb
  • LPC: Ligand-Protein Contacts for 4WF9
  • CSU: Contacts of Structural Units for 4WF9
  • Structure Factors (2912 Kb)
  • Retrieve 4WF9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4WF9 from S2C, [Save to disk]
  • Re-refined 4wf9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4WF9 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 4WF9
  • 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: [4wf9_Y] [4wf9_O] [4wf9_Z] [4wf9_T] [4wf9_A] [4wf9_W] [4wf9_G] [4wf9_N] [4wf9_L] [4wf9_E] [4wf9_D] [4wf9_3] [4wf9_R] [4wf9_M] [4wf9_P] [4wf9_I] [4wf9_J] [4wf9] [4wf9_C] [4wf9_S] [4wf9_2] [4wf9_H] [4wf9_X] [4wf9_K] [4wf9_V] [4wf9_Q] [4wf9_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4WF9: [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
    • Other resources with information on 4WF9
  • Community annotation for 4WF9 at PDBWiki (http://pdbwiki.org)

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