3OMI Oxidoreductase date Aug 27, 2010
title Catalytic Core Subunits (I And II) Of Cytochrome C Oxidase F Rhodobacter Sphaeroides With D132a Mutation
authors J.Liu, L.Qin, S.Ferguson-Miller
compound source
Molecule: Cytochrome C Oxidase, Aa3 Type, Subunit I
Chain: A, C
Fragment: Unp Residues 17-551
Ec: 1.9.3.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Rhodobacter Sphaeroides 2.4.1
Organism_taxid: 272943
Strain: Atcc 170232.4.1ncib 8253dsm 158
Gene: Coxi, Ctad, Rhos4_04590, Rsp_1877
Expression_system: Rhodobacter Sphaeroides
Expression_system_taxid: 1063
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prk415-1

Molecule: Cytochrome C Oxidase Subunit 2
Chain: B, D
Fragment: Unp Residues 30-281
Ec: 1.9.3.1
Engineered: Yes

Organism_scientific: Rhodobacter Sphaeroides 2.4.1
Organism_taxid: 272943
Strain: Atcc 170232.4.1ncib 8253dsm 158
Gene: Coxii, Ctab, Ctac, Rhos4_04060, Rsp_1826
Expression_system: Rhodobacter Sphaeroides
Expression_system_taxid: 1063
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prk415-1
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.064 131.519 175.674 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand CA, CD, CL, CU, CU1, DMU, HEA, HTH, MG, OH, TRD enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
Gene RHOS4 ; RHOS4 ; RSP ; RSP
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • cytochrome-c oxidase activit...


  • D, B
  • cytochrome-c oxidase activit...


  • Primary referenceCrystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump., Liu J, Qin L, Ferguson-Miller S, Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1284-9. Epub 2011 Jan 4. PMID:21205904
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (284 Kb) [Save to disk]
  • Biological Unit Coordinates (3omi.pdb1.gz) 140 Kb
  • Biological Unit Coordinates (3omi.pdb2.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 3OMI
  • CSU: Contacts of Structural Units for 3OMI
  • Structure Factors (2367 Kb)
  • Retrieve 3OMI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OMI from S2C, [Save to disk]
  • Re-refined 3omi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OMI 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 3OMI
  • 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
  • 3D motif for 3OMI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3omi_A] [3omi_D] [3omi] [3omi_B] [3omi_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3OMI
  • Community annotation for 3OMI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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