6KZS | pdb_00006kzs

Crystal structure of cytochrome P450mel 107F1 in complex with heme and imidazole

PDB DOI: https://doi.org/10.2210/pdb6KZS/pdb

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

Deposited: 2019-09-25 Released: 2020-09-23
Deposition Author(s): Hou, X.D., Rao, Y.J., Icyishaka, P., Li, C.X., Lou, J.L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.207 (Depositor), 0.195 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystallization and X-ray analysis of cytochrome P450mel 107F1 with biaryl coupling reactivity

Hou, X.D., Rao, Y.J., Icyishaka, P., Li, C.X., Lou, J.L., Liu, C.M.

To be published.

Macromolecule Content

Total Structure Weight: 47.32 kDa
Atom Count: 3,358
Modeled Residue Count: 396
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P-450	A	412	Streptomyces griseus	Mutation(s): 0 Gene Names: P-450mel, p450-mel, NCTC13033_01802 EC: 1.14
UniProt
Find proteins for Q4H2B8 (Streptomyces griseus) Explore Q4H2B8 Go to UniProtKB: Q4H2B8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4H2B8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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]
IMD Query on IMD 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]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.207 (Depositor), 0.195 (DCC)
R-Value Work: 0.186 (Depositor), 0.187 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.699	α = 90
b = 81.395	β = 90
c = 100.494	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CCP4	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	China	BK20160167
Other private	China	JUSRP51712B
Other private	China	2018YFA090170

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.