2QPE Oxidoreductase date Jul 23, 2007
title An Unexpected Outcome Of Surface-Engineering An Integral Mem Protein: Improved Crystallization Of Cytochrome Ba3 Oxidase Thermus Thermophilus
authors B.Liu, V.M.Luna, Y.Chen, C.D.Stout, J.A.Fee
compound source
Molecule: Cytochrome C Oxidase Subunit 1
Chain: A
Synonym: Cytochrome C Oxidase Polypeptide I, Cytochrome C B Subunit I, Cytochrome Cba3 Subunit 1;
Ec: 1.9.3.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Cbaa
Expression_system: Thermus Thermophilus Hb8
Expression_system_taxid: 300852
Expression_system_strain: Hb8
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmk18

Molecule: Cytochrome C Oxidase Subunit 2
Chain: B
Synonym: Cytochrome C Oxidase Polypeptide II, Cytochrome C Subunit II, Cytochrome Cba3 Subunit 2;
Ec: 1.9.3.1
Engineered: Yes
Mutation: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Cbab, Ctac
Expression_system: Thermus Thermophilus Hb8
Expression_system_taxid: 300852
Expression_system_strain: Hb8
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmk18

Molecule: Cytochrome C Oxidase Polypeptide 2a
Chain: C
Synonym: Cytochrome C Oxidase Polypeptide Iia, Cytochrome C Subunit Iia, Cytochrome Cba3 Subunit 2a;
Ec: 1.9.3.1
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Cbad
Expression_system: Thermus Thermophilus Hb8
Expression_system_taxid: 300852
Expression_system_strain: Hb8
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmk18
symmetry Space Group: P 41 21 2
R_factor 0.234 R_Free 0.302
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.635 114.635 148.568 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand CU1, CUA, HAS, HEM enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • cytochrome-c oxidase activit...


  • B
  • cytochrome-c oxidase activit...


  • C


    Primary referenceAn unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus., Liu B, Luna VM, Chen Y, Stout CD, Fee JA, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Dec 1;63(Pt, 12):1029-34. Epub 2007 Nov 21. PMID:18084085
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (2qpe.pdb1.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 2QPE
  • CSU: Contacts of Structural Units for 2QPE
  • Likely Quarternary Molecular Structure file(s) for 2QPE
  • Structure Factors (336 Kb)
  • Retrieve 2QPE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QPE from S2C, [Save to disk]
  • Re-refined 2qpe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QPE 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 2QPE
  • 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 2QPE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qpe_C] [2qpe_B] [2qpe_A] [2qpe]
  • SWISS-PROT database: [Q5SJ79] [Q5SJ80] [P82543]
  • Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB.
  • Domain organization of [COX1_THET8] [COX2_THET8] [COXA_THET8] by SWISSPFAM
  • Other resources with information on 2QPE
  • Community annotation for 2QPE 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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