2CUA | pdb_00002cua

THE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS

• PDB DOI: https://doi.org/10.2210/pdb2CUA/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1999-02-18 Released: 1999-05-28 
• Deposition Author(s): Williams, P.A., Blackburn, N.J., Sanders, D., Bellamy, H., Stura, E.A., Fee, J.A., Mcree, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.296 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

The CuA domain of Thermus thermophilus ba3-type cytochrome c oxidase at 1.6 A resolution.

Williams, P.A., Blackburn, N.J., Sanders, D., Bellamy, H., Stura, E.A., Fee, J.A., McRee, D.E.

(1999) Nat Struct Biol 6: 509-516

• PubMed: 10360350 
• DOI: https://doi.org/10.1038/9274
• Primary Citation Related Structures: 
  2CUA


• PubMed Abstract: 
  

  The structure of the CuA-containing, extracellular domain of Thermus thermophilus ba3-type cytochrome c oxidase has been determined to 1.6 A resolution using multiple X-ray wavelength anomalous dispersion (MAD). The Cu2S2 cluster forms a planar rhombus with a copper-copper distance of 2.51 +/- 0.03 A. X-ray absorption fine-structure (EXAFS) studies show that this distance is unchanged by crystallization. The CuA center is asymmetrical; one copper is tetrahedrally coordinated to two bridging cysteine thiolates, one histidine nitrogen and one methionine sulfur, while the other is trigonally coordinated by the two cysteine thiolates and a histidine nitrogen. Combined sequence-structure alignment of amino acid sequences reveals conserved interactions between cytochrome c oxidase subunits I and II.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.02 kDa 
• Atom Count: 2,170 
• Modeled Residue Count: 254 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CUA)	A, B	135	Thermus thermophilus	Mutation(s): 0  EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
UniProt
Find proteins for P98052 (Thermus thermophilus) Explore P98052  Go to UniProtKB:  P98052

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CUA	D [auth A], F [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.296 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.9	α = 90
b = 70.6	β = 98.12
c = 53.5	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XTALVIEW	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-28 
Deposition Author(s): Williams, P.A., Blackburn, N.J., Sanders, D., Bellamy, H., Stura, E.A., Fee, J.A., Mcree, D.E.

Revision History  

• Version 1.0: 1999-05-28
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations