PDB-23uh: Structure of the CYP102A1 Heme Domain with 2-(undecylcarbamoyl)be...

ID or keywords:

Entry

Database: PDB / ID: 23uh

Title

Structure of the CYP102A1 Heme Domain with 2-(undecylcarbamoyl)benzoic acid and benzene

Components

Bifunctional cytochrome P450/NADPH--P450 reductase

Keywords

OXIDOREDUCTASE / Monooxygenase

Function / homology

Function and homology information

aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
Similarity search - Function

Biological species

Priestia megaterium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.48 Å

Authors

Ishigami, M. / Sugimoto, H. / Shoji, O.

Funding support

Japan, 4items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP22H05129	Japan
Japan Society for the Promotion of Science (JSPS)	JP22K21346	Japan
Japan Society for the Promotion of Science (JSPS)	JP25H00910	Japan
Japan Science and Technology	JPMJSP2125	Japan

Citation

Journal: To Be Published
Title: Mix-to-Prepare Dicarboxylic Acid-Based Decoy Molecules Enable Wild-Type P450BM3 Catalyzed Oxidation of Non-Native Substrates
Authors: Ishigami, M. / Sugimoto, H. / Shoij, O.

History

Deposition	Feb 18, 2026	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	23uh.cif.gz	395 KB	Display	PDBx/mmCIF format
PDB format	pdb23uh.ent.gz		Display	PDB format
PDBx/mmJSON format	23uh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/3u/23uh ftp://data.pdbj.org/pub/pdb/validation_reports/3u/23uh	HTTPS FTP

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Related structure data

Related structure data	6k58S S: Starting model for refinement
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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (14) #133 - Jan 2011 Nitric Oxide Synthase similarity (10) #82 - Oct 2006 Cytochrome p450 similarity (1)

Deposited unit

A: Bifunctional cytochrome P450/NADPH--P450 reductase

B: Bifunctional cytochrome P450/NADPH--P450 reductase

hetero molecules

107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bifunctional cytochrome P450/NADPH--P450 reductase

hetero molecules

defined by author
Evidence: gel filtration
53.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Bifunctional cytochrome P450/NADPH--P450 reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.714, 128.606, 148.894
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Bifunctional cytochrome P450/NADPH--P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3 Mass: 52300.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: cyp102A1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical	ChemComp-A1MES / 2-(undecylcarbamoyl)benzoic acid Mass: 319.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₂₉NO₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-BNZ / BENZENE Mass: 78.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 816 / 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: 2.7 Å³/Da / Density % sol: 54.43 %
Crystal grow	Temperature: 293 K / Method: batch mode Details: 100 mM Tris-HCl, 120 mM magnesium chloride, 18% w/v PEG8000, 0.5 mM 2-(undecylcarbamoyl)benzoic acid Crystals were soaked in cryobuffer containing benzene.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 16, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.48→46.1 Å / Num. obs: 187855 / % possible obs: 100 % / Redundancy: 13.1 % / B_iso Wilson estimate: 9.52 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.291 / Net I/σ(I): 11.7
Reflection shell	Resolution: 1.48→1.51 Å / Num. unique obs: 9235 / CC_1/2: 0.823

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
X-Area	v Jun 30, 2024	data reduction
Aimless	0.8.2	data scaling
MOLREP	11.9.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6K58

6k58

Resolution: 1.48→46.1 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.956 / SU B: 1.161 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.199	9377	4.994 %
R_work	0.1765	178376	-
all	0.178	-	-
obs	-	187753	99.928 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 15.024 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.084 Å²	0 Å²	-0 Å²
2-	-	0.436 Å²	0 Å²
3-	-	-	-0.351 Å²

Refinement step

Cycle: LAST / Resolution: 1.48→46.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7342	0	144	816	8302

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	7758
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7346
X-RAY DIFFRACTION	r_angle_refined_deg	1.984	1.872	10523
X-RAY DIFFRACTION	r_angle_other_deg	0.677	1.788	16975
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.336	5	928
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.866	5	60
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.108	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.393	10	1376
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.145	10	373
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1114
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	9122
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1742
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	1624
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	6627
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	3788
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	4008
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	554
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.004	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.103	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.146	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.088	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	1.532	1.262	3688
X-RAY DIFFRACTION	r_mcbond_other	1.532	1.262	3688
X-RAY DIFFRACTION	r_mcangle_it	2.27	2.261	4624
X-RAY DIFFRACTION	r_mcangle_other	2.271	2.261	4625
X-RAY DIFFRACTION	r_scbond_it	2.683	1.539	4070
X-RAY DIFFRACTION	r_scbond_other	2.683	1.539	4069
X-RAY DIFFRACTION	r_scangle_it	4.164	2.682	5899
X-RAY DIFFRACTION	r_scangle_other	4.163	2.681	5900
X-RAY DIFFRACTION	r_lrange_it	5.05	12.642	8979
X-RAY DIFFRACTION	r_lrange_other	4.952	12.045	8818

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 (%)
1.48-1.518	0.245	709	0.225	13043	X-RAY DIFFRACTION	99.9201
1.518-1.56	0.231	655	0.205	12680	X-RAY DIFFRACTION	99.9101
1.56-1.605	0.228	624	0.192	12442	X-RAY DIFFRACTION	99.9617
1.605-1.654	0.201	628	0.176	12044	X-RAY DIFFRACTION	99.9606
1.654-1.709	0.202	593	0.171	11726	X-RAY DIFFRACTION	99.9757
1.709-1.769	0.211	603	0.18	11264	X-RAY DIFFRACTION	99.9158
1.769-1.835	0.217	592	0.187	10956	X-RAY DIFFRACTION	99.9654
1.835-1.91	0.219	563	0.185	10453	X-RAY DIFFRACTION	99.8821
1.91-1.995	0.211	559	0.18	10064	X-RAY DIFFRACTION	99.9342
1.995-2.092	0.196	530	0.191	9649	X-RAY DIFFRACTION	99.9019
2.092-2.205	0.208	464	0.188	9219	X-RAY DIFFRACTION	99.9278
2.205-2.338	0.2	464	0.175	8732	X-RAY DIFFRACTION	99.8805
2.338-2.499	0.2	433	0.177	8158	X-RAY DIFFRACTION	99.8605
2.499-2.699	0.221	405	0.177	7705	X-RAY DIFFRACTION	99.9507
2.699-2.955	0.209	379	0.171	7068	X-RAY DIFFRACTION	99.9463
2.955-3.303	0.179	333	0.165	6449	X-RAY DIFFRACTION	99.9411
3.303-3.81	0.167	292	0.159	5715	X-RAY DIFFRACTION	99.9834
3.81-4.659	0.148	239	0.145	4881	X-RAY DIFFRACTION	99.9805
4.659-6.555	0.195	201	0.177	3851	X-RAY DIFFRACTION	100
6.555-46.1	0.163	111	0.164	2278	X-RAY DIFFRACTION	99.9164

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