4FA7

Structure of Recombinant Cytochrome ba3 Oxidase mutant A204F from Thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb4FA7/pdb

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

Deposited: 2012-05-21 Released: 2012-05-30
Deposition Author(s): Li, Y., Chen, Y., Stout, C.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.220
R-Value Work: 0.169
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 93.3 kDa
Atom Count: 6,393
Modelled Residue Count: 743
Deposited Residue Count: 770
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A	568	Thermus thermophilus HB8	Mutation(s): 1 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SJ79
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SJ80
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P82543
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HAS Query on HAS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	HEME-AS C₅₄ H₆₄ Fe N₄ O₆ PDYODZVCODUKFH-ZOMLSHGTSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth C] SDF format, chain L [auth A] SDF format, chain R [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth C] MOL2 format, chain L [auth A] MOL2 format, chain R [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] 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], R [auth A], S [auth A], U [auth B], V [auth B], W [auth B], X [auth C]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEO Query on PEO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.220
R-Value Work: 0.169
R-Value Observed: 0.172
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.55	α = 90
b = 98.21	β = 127.92
c = 94.86	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-05-30

Deposition Author(s):

Li, Y.

Chen, Y.

Stout, C.D.

Revision History (Full details and data files)

Version 1.0: 2012-05-30
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description