2QPE

An unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus

Structural Biology Knowledgebase: 2QPE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302
  • R-Value Work: 0.234

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2QPE

Classification: Oxidoreductase

Total Structure Weight: 87509.01

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome c oxidase subunit 1 A 568 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Mutation: K258R
Gene Name(s): cbaA TTHA1135
Cytochrome c oxidase subunit 2 B 168 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Mutation: E4Q
Gene Name(s): cbaB ctaC TTHA1134
Cytochrome c oxidase polypeptide 2A C 34 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Gene Name(s): cbaD TTHA1133

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)

Protein Name: Cytochrome ba3


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HAS
Query on HAS

A HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CUA
Query on CUA

B DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU1
Query on CU1

A COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302
  • R-Value Work: 0.234
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 114.64 α = 90.00
b = 114.64 β = 90.00
c = 148.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-23
  • Released Date: 2007-12-11
  • Deposition author(s): Liu, B., Luna, V.M., Chen, Y., Stout, C.D., Fee, J.A.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor