Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87879.46 
• Atom Count: 6102 
• Residue Count: 770 
• Unique protein chains: 3

1XME

Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus

• DOI: 10.2210/pdb1XME/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
• Expression System: Thermus thermophilus HB8


• Deposited: 2004-10-01 Released: 2005-03-22 
• Deposition Author(s): Hunsicker-Wang, L.M., Pacoma, R.L., Chen, Y., Fee, J.A., Stout, C.D.

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Experimental Data Snapshot

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

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

• PubMed: 15735345 
• 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 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%.

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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
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome c oxidase polypeptide I	A	568	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: cbaA EC: 1.9.3.1
Find proteins for Q5SJ79 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SJ79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome c oxidase polypeptide II	B	168	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: cbaB (ctaC) EC: 1.9.3.1
Find proteins for Q5SJ80 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SJ80

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome c oxidase polypeptide IIA	C	34	Thermus 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HAS	A	HEME-AS C54 H64 Fe N4 O6 PDYODZVCODUKFH-QIHJKJTBDH
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CUA	B	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CU	A	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
BNG	A	B-NONYLGLUCOSIDE C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N

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 = 114.902	α = 90.00
b = 114.902	β = 90.00
c = 177.064	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
MOLREP	phasing
CNS	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-01 
• Released Date: 2005-03-22 
• Deposition Author(s): Hunsicker-Wang, L.M., Pacoma, R.L., Chen, Y., Fee, J.A., Stout, C.D.

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