4G7Q

Structure of Recombinant Cytochrome ba3 Oxidase mutant V236L from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb4G7Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Thermus thermophilus
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2012-07-20 Released: 2013-07-24 
• Deposition Author(s): Li, Y., Chen, Y., Stout, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Literature

Structure of Recombinant Cytochrome ba3 Oxidase mutant V236L from Thermus thermophilus

Li, Y., Chen, Y., Stout, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 93.45 kDa 
• Atom Count: 6,385 
• Modelled Residue Count: 752 
• Deposited Residue Count: 771 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A	569	Thermus thermophilus HB8	Mutation(s): 2  Gene Names: cbaA, TTHA1135 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for Q5SJ79 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ79  Go to UniProtKB:  Q5SJ79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B	168	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaB, ctaC, TTHA1134 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for Q5SJ80 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ80  Go to UniProtKB:  Q5SJ80

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide 2A	C	34	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaD, TTHA1133 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P82543 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P82543  Go to UniProtKB:  P82543

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HAS	F [auth A]	HEME-AS C54 H64 Fe N4 O6 PDYODZVCODUKFH-ZOMLSHGTSA-L
HEM	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OLC	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth C], X [auth C]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
CUA	R [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
CU	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
PER	G [auth A]	PEROXIDE ION O2 ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.67	α = 90
b = 98.18	β = 127.82
c = 94.56	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Li, Y., Chen, Y., Stout, C.D.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Non-polymer description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations