3MK7 | pdb_00003mk7

The structure of CBB3 cytochrome oxidase

PDB DOI: https://doi.org/10.2210/pdb3MK7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Stutzerimonas stutzeri
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2010-04-14 Released: 2010-08-04
Deposition Author(s): Buschmann, S., Warkentin, E., Michel, H., Ermler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.223 (Depositor), 0.232 (DCC)
R-Value Work:
0.189 (Depositor), 0.198 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Structure of cbb3 Cytochrome Oxidase Provides Insights into Proton Pumping

Buschmann, S., Warkentin, E., Xie, H., Langer, J.D., Ermler, U., Michel, H.

(2010) Science 329: 327-330

PubMed: 20576851 Search on PubMed
DOI: https://doi.org/10.1126/science.1187303
Primary Citation Related Structures:
3MK7, 5DJQ

PubMed Abstract:
The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 reduction and transmembrane proton pumping. To gain new insights into the still enigmatic process, we structurally characterized a C-family HCO--essential for the pathogenicity of many bacteria--that differs from the two other HCO families, A and B, that have been structurally analyzed. The x-ray structure of the C-family cbb3 oxidase from Pseudomonas stutzeri at 3.2 angstrom resolution shows an electron supply system different from families A and B. Like family-B HCOs, C HCOs have only one pathway, which conducts protons via an alternative tyrosine-histidine cross-link. Structural differences around hemes b and b3 suggest a different redox-driven proton-pumping mechanism and provide clues to explain the higher activity of family-C HCOs at low oxygen concentrations.

Organizational Affiliation

Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt/Main, Germany.

Macromolecule Content

Total Structure Weight: 462.03 kDa
Atom Count: 31,690
Modeled Residue Count: 3,979
Deposited Residue Count: 4,072
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase, cbb3-type, subunit N	A, D, G, J [auth K]	474	Stutzerimonas stutzeri	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for D9IA43 (Stutzerimonas stutzeri) Explore D9IA43 Go to UniProtKB: D9IA43
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9IA43
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase, cbb3-type, subunit O	B, E, H, K [auth L]	203	Stutzerimonas stutzeri	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D9IA44 (Stutzerimonas stutzeri) Explore D9IA44 Go to UniProtKB: D9IA44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9IA44
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase, cbb3-type, subunit P	C, F, I, L [auth M]	311	Stutzerimonas stutzeri	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D9IA45 (Stutzerimonas stutzeri) Explore D9IA45 Go to UniProtKB: D9IA45
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9IA45
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30-mer peptide	M [auth U], N [auth X], O [auth Y], P [auth Z]	30	Stutzerimonas stutzeri	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain EB [auth L] SDF format, chain GB [auth M] SDF format, chain HB [auth M] SDF format, chain IA [auth E] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain TA [auth H] SDF format, chain VA [auth I] SDF format, chain WA [auth I] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain EB [auth L] MOL2 format, chain GB [auth M] MOL2 format, chain HB [auth M] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain TA [auth H] MOL2 format, chain VA [auth I] MOL2 format, chain WA [auth I] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain EB [auth L] mmCIF format, chain GB [auth M] mmCIF format, chain HB [auth M] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain TA [auth H] mmCIF format, chain VA [auth I] mmCIF format, chain WA [auth I] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	EB [auth L] GB [auth M] HB [auth M] IA [auth E] JA [auth F] EB [auth L], GB [auth M], HB [auth M], IA [auth E], JA [auth F], KA [auth F], TA [auth H], VA [auth I], WA [auth I], X [auth B], Y [auth C], Z [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain EB [auth L] Focus chain GB [auth M] Focus chain HB [auth M] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain TA [auth H] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EB [auth L] Focus chain GB [auth M] Focus chain HB [auth M] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain TA [auth H] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain XA [auth K] SDF format, chain YA [auth K] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain XA [auth K] MOL2 format, chain YA [auth K] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain XA [auth K] mmCIF format, chain YA [auth K]	BA [auth D] CA [auth D] MA [auth G] NA [auth G] Q [auth A] BA [auth D], CA [auth D], MA [auth G], NA [auth G], Q [auth A], R [auth A], XA [auth K], YA [auth K]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain Q [auth A] Focus chain R [auth A] Focus chain XA [auth K] Focus chain YA [auth K] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain Q [auth A] Focus chain R [auth A] Focus chain XA [auth K] Focus chain YA [auth K]
FC6 Query on FC6 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FB [auth M] SDF format, chain LA [auth F] SDF format, chain UA [auth I] MOL2 format, chain AA [auth C] MOL2 format, chain FB [auth M] MOL2 format, chain LA [auth F] MOL2 format, chain UA [auth I] mmCIF format, chain AA [auth C] mmCIF format, chain FB [auth M] mmCIF format, chain LA [auth F] mmCIF format, chain UA [auth I]	AA [auth C], FB [auth M], LA [auth F], UA [auth I]	HEXACYANOFERRATE(3-) C₆ Fe N₆ HCMVSLMENOCDCK-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FB [auth M] Focus chain LA [auth F] Focus chain UA [auth I] Interactions & Density Focus chain AA [auth C] Focus chain FB [auth M] Focus chain LA [auth F] Focus chain UA [auth I]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain CB [auth K] SDF format, chain FA [auth D] SDF format, chain SA [auth G] SDF format, chain V [auth A] MOL2 format, chain CB [auth K] MOL2 format, chain FA [auth D] MOL2 format, chain SA [auth G] MOL2 format, chain V [auth A] mmCIF format, chain CB [auth K] mmCIF format, chain FA [auth D] mmCIF format, chain SA [auth G] mmCIF format, chain V [auth A]	CB [auth K], FA [auth D], SA [auth G], V [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CB [auth K] Focus chain FA [auth D] Focus chain SA [auth G] Focus chain V [auth A] Interactions & Density Focus chain CB [auth K] Focus chain FA [auth D] Focus chain SA [auth G] Focus chain V [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain OA [auth G] SDF format, chain S [auth A] SDF format, chain ZA [auth K] MOL2 format, chain DA [auth D] MOL2 format, chain OA [auth G] MOL2 format, chain S [auth A] MOL2 format, chain ZA [auth K] mmCIF format, chain DA [auth D] mmCIF format, chain OA [auth G] mmCIF format, chain S [auth A] mmCIF format, chain ZA [auth K]	DA [auth D], OA [auth G], S [auth A], ZA [auth K]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain OA [auth G] Focus chain S [auth A] Focus chain ZA [auth K] Interactions & Density Focus chain DA [auth D] Focus chain OA [auth G] Focus chain S [auth A] Focus chain ZA [auth K]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BB [auth K] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain PA [auth G] SDF format, chain T [auth A] SDF format, chain W [auth B] SDF format, chain QA [auth G] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth K] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain PA [auth G] MOL2 format, chain T [auth A] MOL2 format, chain W [auth B] MOL2 format, chain QA [auth G] mmCIF format, chain AB [auth K] mmCIF format, chain BB [auth K] mmCIF format, chain EA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain PA [auth G] mmCIF format, chain T [auth A] mmCIF format, chain W [auth B] mmCIF format, chain QA [auth G]	AB [auth K] BB [auth K] EA [auth D] HA [auth E] PA [auth G] AB [auth K], BB [auth K], EA [auth D], HA [auth E], PA [auth G], QA [auth G], T [auth A], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain BB [auth K] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain T [auth A] Focus chain W [auth B] Interactions & Density Focus chain AB [auth K] Focus chain BB [auth K] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain T [auth A] Focus chain W [auth B]
PEO Query on PEO Download:Ideal Coordinates CCD File SDF format, chain DB [auth K] SDF format, chain GA [auth D] SDF format, chain RA [auth G] SDF format, chain U [auth A] MOL2 format, chain DB [auth K] MOL2 format, chain GA [auth D] MOL2 format, chain RA [auth G] MOL2 format, chain U [auth A] mmCIF format, chain DB [auth K] mmCIF format, chain GA [auth D] mmCIF format, chain RA [auth G] mmCIF format, chain U [auth A]	DB [auth K], GA [auth D], RA [auth G], U [auth A]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth K] Focus chain GA [auth D] Focus chain RA [auth G] Focus chain U [auth A] Interactions & Density Focus chain DB [auth K] Focus chain GA [auth D] Focus chain RA [auth G] Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.223 (Depositor), 0.232 (DCC)
R-Value Work: 0.189 (Depositor), 0.198 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.475	α = 90
b = 279.933	β = 90
c = 175.192	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary