4WQ0 | pdb_00004wq0

Crystal structure of cytochrome P450 CYP107W1 from Streptomyces avermitilis in complex with Oligomycin A

PDB DOI: https://doi.org/10.2210/pdb4WQ0/pdb

Classification: OXIDOREDUCTASE/ANTIBIOTIC
Organism(s): Streptomyces avermitilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-10-21 Released: 2015-10-28
Deposition Author(s): Kang, L.W., Kim, D.H., Pham, T.V., Han, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.288 (Depositor), 0.280 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of cytochrome P450 CYP107W1 from Streptomyces avermitilis in complex with Oligomycin A

Kang, L.W., Kim, D.H., Pham, T.V., Han, S.H., Kim, J.H., Lim, Y.R., Park, H.G., Cha, G.S., Yun, C.H., Chun, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 44.72 kDa
Atom Count: 3,157
Modelled Residue Count: 397
Deposited Residue Count: 397
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	397	Streptomyces avermitilis	Mutation(s): 0 Gene Names: olmB
UniProt
Find proteins for Q93HJ0 (Streptomyces avermitilis) Explore Q93HJ0 Go to UniProtKB: Q93HJ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93HJ0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EFO Query on EFO 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]	Oligomycin A C₄₅ H₇₄ O₁₁ MNULEGDCPYONBU-AWJDAWNUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.288 (Depositor), 0.280 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.812	α = 90
b = 127.812	β = 90
c = 76.584	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data reduction
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.