7WZL | pdb_00007wzl

Crystal structure of Cytochrome P450 184A1 from streptomyces avermitilis

PDB DOI: https://doi.org/10.2210/pdb7WZL/pdb

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

Deposited: 2022-02-18 Released: 2023-02-22
Deposition Author(s): Kim, V.C., Kim, D.G., Lee, S.G., Lee, G.H., Lee, S.A., Kang, L.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.251 (Depositor), 0.260 (DCC)
R-Value Work:
0.204 (Depositor), 0.220 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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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 184A1 from streptomyces avermitilis

Kim, V.C., Kim, D.G., Lee, S.G., Lee, G.H., Lee, S.A., Kang, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 54.39 kDa
Atom Count: 3,484
Modeled Residue Count: 450
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cytochrome P450	A	492	Streptomyces avermitilis	Mutation(s): 0 Gene Names: cyp21, SAVERM_5111
UniProt
Find proteins for Q82D73 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82D73 Go to UniProtKB: Q82D73
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82D73
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) 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: 2.27 Å
R-Value Free: 0.251 (Depositor), 0.260 (DCC)
R-Value Work: 0.204 (Depositor), 0.220 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.668	α = 90
b = 62.071	β = 90
c = 134.296	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.