8B4O | pdb_00008b4o

Cryo-EM structure of cytochrome bd oxidase from C. glutamicum

PDB DOI: https://doi.org/10.2210/pdb8B4O/pdb
EM Map EMD-15851: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium glutamicum
Expression System: Corynebacterium glutamicum
Mutation(s): No
Membrane Protein: Yes OPM PDBTM

Deposited: 2022-09-20 Released: 2022-12-28
Deposition Author(s): Grund, T.N., Kusumoto, T., Michel, H., Sakamoto, J., Safarian, S.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8B4O

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

Literature

Cryo-EM structure of cytochrome bd oxidase from C. glutamicum

Grund, T.N., Michel, H., Safarian, S.

To be published.

Macromolecule Content

Total Structure Weight: 94.81 kDa
Atom Count: 6,156
Modeled Residue Count: 772
Deposited Residue Count: 846
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bd-type quinol oxidase subunit II	A [auth B]	333	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: cydB, CS176_1127

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome BD ubiquinol oxidase subunit I	B [auth A]	513	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: cydA, BBD29_06150 Membrane Entity: Yes
UniProt
Find proteins for Q9KWL8 (Corynebacterium glutamicum) Explore Q9KWL8 Go to UniProtKB: Q9KWL8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KWL8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HDD (Subject of Investigation/LOI) Query on HDD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C₃₄ H₃₂ Fe N₄ O₅ UMGOPAWIGKFTRK-QQDQPIDJSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
HEB (Subject of Investigation/LOI) Query on HEB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	HEME B/C C₃₄ H₃₄ Fe N₄ O₄ NEGHHAJBRZGUAY-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2022-12-28
Type: Initial release
Version 1.1: 2024-07-24
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.