1XME

Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus.

Hunsicker-Wang, L.M., Pacoma, R.L., Chen, Y., Fee, J.A., Stout, C.D.

(2005) Acta Crystallogr.,Sect.D 61: 340-343

  • DOI: 10.1107/S0907444904033906
  • Also Cited By: 3EH5, 3EH4, 3EH3, 3BVD

  • PubMed Abstract: 

    • Cytochrome ba(3) oxidase is an integral membrane protein identified in the thermophilic bacterium Thermus thermophilus. The enzyme has now been expressed recombinantly and purified with a histidine tag. As such, it crystallizes under similar conditio ...

    Cytochrome ba(3) oxidase is an integral membrane protein identified in the thermophilic bacterium Thermus thermophilus. The enzyme has now been expressed recombinantly and purified with a histidine tag. As such, it crystallizes under similar conditions and in the same space group (P4(3)2(1)2) as the native protein. A novel cryoprotection scheme is described here to obtain high-resolution diffraction from these crystals, which involves soaking in a mixture of glycerol and ethylene glycol under a layer of oil. The unit-cell parameters for these crystals are larger than the native protein, apparently deriving from increased ordering of the N-terminus and an internal loop (residues 495-500) in subunit I. Hence, compared with native cytochrome ba(3) oxidase, the recombinant His-tagged protein is accommodated in an expanded but equally well ordered lattice via an alternate set of specific intermolecular contacts. The structure was refined against data to 2.3 angstroms resolution to an R factor of 21.7% and an R(free) of 23.7%.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, MB8, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide I
A
568Thermus thermophilusMutation(s): 0 
Gene Names: cbaA
EC: 1.9.3.1
Find proteins for Q56408 (Thermus thermophilus)
Go to UniProtKB:  Q56408
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide II
B
168Thermus thermophilusMutation(s): 0 
Gene Names: cbaB (ctaC)
EC: 1.9.3.1
Find proteins for P98052 (Thermus thermophilus)
Go to UniProtKB:  P98052
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide IIA
C
34Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: cbaD
EC: 1.9.3.1
Find proteins for P82543 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P82543
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAS
Query on HAS
Download SDF File 
Download CCD File 
A
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CUA
Query on CUA
Download SDF File 
Download CCD File 
B
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CU
Query on CU
Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
BNG
Query on BNG
Download SDF File 
Download CCD File 
A
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.902α = 90.00
b = 114.902β = 90.00
c = 177.064γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOLREPphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance