PDB-9yv5: Crystal structure of cytochrome P450 enzyme Bmp7

ID or keywords:

Entry

Database: PDB / ID: 9yv5

Title

Crystal structure of cytochrome P450 enzyme Bmp7

Components

Polybrominated aromatic compounds synthase

Keywords

OXIDOREDUCTASE / cytochrome P450 enzyme / biaryl coupling

Function / homology

Function and homology information

Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of water / steroid 17-alpha-monooxygenase activity / hormone biosynthetic process / progesterone metabolic process / iron ion binding / heme binding
Similarity search - Function

Biological species

Marinomonas mediterranea (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Nolan, K. / Wang, Y.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM147510	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM128742	United States

Citation

Journal: Acs Catalysis / Year: 2025
Title: Bacterial Cytochrome P450 for Oxidative Halogenated Biaryl Coupling
Authors: Petriti, V. / Nolan, K. / Xu, W. / Tsai, S. / Wang, X. / Xie, W.J. / Zheng, G. / Wang, Y. / Ding, Y.

History

Deposition	Oct 23, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 7, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yv5.cif.gz	118.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9yv5.ent.gz	88.4 KB	Display	PDB format
PDBx/mmJSON format	9yv5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9yv5_validation.pdf.gz	811.2 KB	Display	wwPDB validaton report
Full document	9yv5_full_validation.pdf.gz	815.1 KB	Display
Data in XML	9yv5_validation.xml.gz	25.3 KB	Display
Data in CIF	9yv5_validation.cif.gz	35.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/9yv5 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/9yv5	HTTPS FTP

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Related structure data

Related structure data	9ms3C 9yvvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#155 - Nov 2012 Vitamin D Receptor similarity (1)

Deposited unit

A: Polybrominated aromatic compounds synthase

hetero molecules

57.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	101.270, 101.270, 159.692
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Polybrominated aromatic compounds synthase / CYP450 Bmp7 Mass: 56486.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinomonas mediterranea (bacteria) / Gene: bmp7, Marme_4095 / Production host: Escherichia coli (E. coli) References: UniProt: F2K081, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of water
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.18 Å³/Da / Density % sol: 70.61 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350 and 0.2 M of sodium citrate tribasic dihydrate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2025

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.28→50 Å / Num. obs: 43400 / % possible obs: 98.9 % / Redundancy: 4 % / CC_1/2: 0.987 / CC star: 0.997 / R_merge(I) obs: 0.148 / R_pim(I) all: 0.081 / R_rim(I) all: 0.169 / Χ²: 1.122 / Net I/σ(I): 5.8 / Num. measured all: 175267

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.28-2.32	3.4	0.84	1984	0.731	0.919	0.47	0.971	0.962	93.2
2.32-2.36	3.6	1.028	2086	0.666	0.894	0.573	1.185	0.991	96.2
2.36-2.41	3.8	1.046	2132	0.579	0.856	0.584	1.205	0.958	98.6
2.41-2.46	4.1	1.02	2157	0.62	0.875	0.568	1.173	0.974	99.2
2.46-2.51	4.2	0.878	2124	0.686	0.902	0.489	1.01	0.986	99.5
2.51-2.57	4.2	0.722	2170	0.791	0.94	0.401	0.829	0.986	99.7
2.57-2.63	4.2	0.631	2159	0.822	0.95	0.351	0.725	1.037	99.8
2.63-2.7	4.1	0.55	2178	0.833	0.953	0.308	0.633	1.012	99.8
2.7-2.78	4.1	0.489	2164	0.871	0.965	0.275	0.564	1.043	99.8
2.78-2.87	4.1	0.37	2171	0.912	0.977	0.208	0.427	1.06	99.6
2.87-2.98	4.1	0.311	2185	0.944	0.986	0.174	0.358	1.051	99.7
2.98-3.09	4	0.224	2169	0.97	0.992	0.125	0.257	1.079	99.7
3.09-3.24	4	0.187	2170	0.97	0.992	0.105	0.216	1.137	99.5
3.24-3.41	4	0.137	2187	0.989	0.997	0.076	0.158	1.151	99.5
3.41-3.62	4.3	0.109	2195	0.991	0.998	0.058	0.124	1.225	99.5
3.62-3.9	4.2	0.083	2208	0.995	0.999	0.044	0.094	1.353	99.5
3.9-4.29	4.2	0.069	2191	0.995	0.999	0.036	0.078	1.354	99.5
4.29-4.91	4.1	0.06	2215	0.995	0.999	0.032	0.069	1.375	99.6
4.91-6.19	4.1	0.057	2221	0.996	0.999	0.031	0.065	1.251	98.5
6.19-50	4	0.045	2334	0.997	0.999	0.024	0.051	1.305	97.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
SCALEPACK		data scaling
DENZO		data reduction
PHENIX		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.28→48.27 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2485	1982	4.66 %
R_work	0.1996	-	-
obs	0.2018	42533	97.03 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.28→48.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3877	0	0	296	4173

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3971
X-RAY DIFFRACTION	f_angle_d	0.84	5378
X-RAY DIFFRACTION	f_dihedral_angle_d	8.557	526
X-RAY DIFFRACTION	f_chiral_restr	0.048	563
X-RAY DIFFRACTION	f_plane_restr	0.007	695

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.28-2.34	0.3518	131	0.3469	2585	X-RAY DIFFRACTION	89
2.34-2.4	0.3018	130	0.3341	2781	X-RAY DIFFRACTION	94
2.4-2.47	0.3352	134	0.3096	2842	X-RAY DIFFRACTION	96
2.47-2.55	0.2949	144	0.2891	2854	X-RAY DIFFRACTION	97
2.55-2.64	0.3048	142	0.2595	2829	X-RAY DIFFRACTION	97
2.64-2.75	0.2526	142	0.2553	2908	X-RAY DIFFRACTION	98
2.75-2.87	0.325	140	0.2317	2878	X-RAY DIFFRACTION	98
2.87-3.02	0.2818	147	0.2358	2907	X-RAY DIFFRACTION	98
3.02-3.21	0.2745	141	0.2118	2936	X-RAY DIFFRACTION	98
3.21-3.46	0.2733	145	0.2028	2942	X-RAY DIFFRACTION	99
3.46-3.81	0.2001	145	0.1699	2988	X-RAY DIFFRACTION	99
3.81-4.36	0.1868	145	0.1456	2976	X-RAY DIFFRACTION	99
4.36-5.49	0.1921	144	0.1489	3023	X-RAY DIFFRACTION	99
5.49-48.27	0.2608	152	0.1735	3102	X-RAY DIFFRACTION	97

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