8HOT | pdb_00008hot

Crystal structure of the P450 BM3 heme domain mutant F87A in complex with NH2-C7-Phe-Phe

PDB DOI: https://doi.org/10.2210/pdb8HOT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-12-10 Released: 2023-12-13
Deposition Author(s): Jiang, Y., Dong, S., Feng, Y., Cong, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of the P450 BM3 heme domain mutant F87A in complex with NH2-C7-Phe-Phe

Jiang, Y., Dong, S., Feng, Y., Cong, Z.

To be published.

Macromolecule Content

Total Structure Weight: 108.82 kDa
Atom Count: 8,107
Modeled Residue Count: 899
Deposited Residue Count: 936
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	465	Priestia megaterium	Mutation(s): 1 Gene Names: BTA37_15100 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779 Go to UniProtKB: P14779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NH2-C7-Phe-Phe	C, D	3	synthetic construct	Mutation(s): 0

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 E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.723	α = 90
b = 146.446	β = 97.48
c = 63.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
autoPROC	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22207112
National Natural Science Foundation of China (NSFC)	China	21977104

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary

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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.