PDB-3ben: Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bou...

ID or keywords:

Entry

Database: PDB / ID: 3ben

Title

Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme domain of Cytochrome P450-BM3

Components

Cytochrome P450 102

Keywords

OXIDOREDUCTASE / PROTEIN-SUBSTRATE COMPLEX / HEMEPROTEIN / Electron transport / FAD / Flavoprotein / FMN / Iron / Membrane / Metal-binding / Monooxygenase / Multifunctional enzyme / NADP / Transport

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

Bacillus megaterium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.65 Å

Authors

Tomchick, D.R.

Citation

Journal: Biochemistry / Year: 2008
Title: Crystal structure of inhibitor-bound P450BM-3 reveals open conformation of substrate access channel.
Authors: Haines, D.C. / Chen, B. / Tomchick, D.R. / Bondlela, M. / Hegde, A. / Machius, M. / Peterson, J.A.

History

Deposition	Nov 19, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ben.cif.gz	227 KB	Display	PDBx/mmCIF format
PDB format	pdb3ben.ent.gz	180.9 KB	Display	PDB format
PDBx/mmJSON format	3ben.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/be/3ben ftp://data.pdbj.org/pub/pdb/validation_reports/be/3ben	HTTPS FTP

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Related structure data

Related structure data	1jpzS 1bu7 S: Starting model for refinement
Similar structure data	6h1s-1 4duf-2 6l1a-1 4dtw-2 4dtz-1 3npl-1 3dgi-1 4due-1 4kpb-2 6js8-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Cytochrome P450 102

B: Cytochrome P450 102

hetero molecules

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

1

A: Cytochrome P450 102

hetero molecules

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

2

B: Cytochrome P450 102

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.820, 148.209, 63.792
Angle α, β, γ (deg.)	90.00, 98.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Cytochrome P450 102 Mass: 53671.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A1, cyp102 / Plasmid: PPROEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5(ALPHA)F'IQ / References: UniProt: P14779, unspecific monooxygenase

#1: Protein

Cytochrome P450 102

Mass: 53671.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus megaterium (bacteria) / Gene: CYP102A1, cyp102 / Plasmid: PPROEX-1 / Production host:

Escherichia coli (E. coli) / Strain (production host): DH5(ALPHA)F'IQ / References: UniProt: P14779, unspecific monooxygenase

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Non-polymers , 5 types, 910 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-LEH / N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine Type: L-peptide linking / Mass: 379.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₇N₃O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 904 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 52.01 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 11% (w/v) PEG-3350, 200 mM magnesium chloride, 7.5% (v/v) glycerol, 100 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97959 Å
Detector	Detector: CCD / Date: Jun 10, 2004
Radiation	Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97959 Å / Relative weight: 1
Reflection	Resolution: 1.65→35.2 Å / Num. all: 125826 / Num. obs: 125826 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / B_iso Wilson estimate: 17.6 Å² / R_merge(I) obs: 0.048 / Net I/σ(I): 26.1
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.249 / Mean I/σ(I) obs: 4.4 / Num. unique all: 5307 / % possible all: 81.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
CNS		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB entry 1JPZ

1jpz

Resolution: 1.65→30 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.955 / SU B: 2.927 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19125	3825	3 %	RANDOM
R_work	0.16122	-	-	-
all	0.16214	121940	-	-
obs	0.16214	121940	97.24 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 18.795 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.12 Å²	0 Å²	-0.11 Å²
2-	-	-0.62 Å²	0 Å²
3-	-	-	1.71 Å²

Refine analyze

Luzzati sigma a obs: 0.053 Å

Refinement step

Cycle: LAST / Resolution: 1.65→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7332	0	153	904	8389

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	8005
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.695	2.043	10905
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.855	5	959
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.2	24.947	380
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.251	15	1409
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.036	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	1131
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6177
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	3994
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	5561
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	795
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.184	0.2	2
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.16	0.2	54
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.131	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.464	2	4817
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.095	3	7638
X-RAY DIFFRACTION	r_scbond_it	1.842	2	3559
X-RAY DIFFRACTION	r_scangle_it	2.752	3	3259
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.215	245	-
R_work	0.168	7694	-
obs	-	3825	83.25 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.8834	0.1421	-0.3575	0.7203	-0.0142	3.1705	0.0128	-0.2864	0.1634	0.0621	-0.058	-0.0123	-0.0674	0.0324	0.0452	0.0107	-0.0021	0.0206	0.0961	-0.0603	0.0049	13.2259	15.7278	28.721
2	0.857	0.4983	0.2295	0.7406	0.1586	0.2922	0.0446	-0.0667	-0.0784	0.0744	0.0049	0.013	0.0135	0.0363	-0.0494	0.027	0.0027	0.0188	0.0268	0.0192	0.0286	20.3748	-6.4483	11.3604
3	2.0558	0.2552	-1.0666	2.0621	0.5948	4.8175	0.2702	-0.4128	-0.119	0.4918	-0.0532	-0.0178	0.0758	-0.2086	-0.217	0.1347	-0.0807	-0.0607	0.0627	0.1106	-0.0052	25.6074	-11.3544	27.9506
4	3.5036	1.0678	-0.9503	0.9283	-0.3931	1.5366	-0.0734	0.1664	-0.3524	-0.067	0.0419	-0.1949	0.1909	-0.0149	0.0314	0.0412	0.0046	0.0054	0.0167	-0.0033	0.0644	33.2715	-7.6817	9.7155
5	1.0051	0.2608	0.3522	0.4944	0.2505	0.6412	0.001	-0.053	0.1067	-0.0481	-0.0143	0.0032	-0.0945	-0.039	0.0134	0.0494	0.0086	0.018	0.0484	0.0069	0.0191	8.7808	6.7671	7.905
6	1.4244	0.7241	0.5838	0.7942	0.5116	0.6137	-0.0445	0.073	0.0376	-0.0996	0.062	0.0451	-0.0919	0.0227	-0.0175	0.0569	-0.005	0.0096	0.059	0.0115	0.0216	14.6547	1.3886	4.2478
7	1.4751	0.673	0.2876	1.9784	0.8477	1.7481	0.0196	-0.0724	-0.1505	0.0643	-0.0144	0.0575	0.1139	0.0085	-0.0052	0.048	0.0086	0.0072	0.0685	0.0354	0.0368	-0.4233	-9.1885	12.6617
8	1.5416	-0.0665	0.4572	0.7718	-0.5038	3.1706	0.0192	0.2491	-0.1257	-0.1054	-0.0477	-0.0293	0.1618	0.2229	0.0285	0.0397	0.0028	-0.0047	0.0868	-0.0479	0.0045	-6.8971	7.8318	-31.2498
9	0.8338	-0.6489	-0.1446	0.8259	0.1461	0.1493	-0.0225	0.0084	0.0726	-0.0697	0.0121	0.0106	-0.0172	0.0715	0.0104	0.0305	-0.0076	-0.0117	0.0326	-0.0047	0.015	3.4201	25.8183	-12.4669
10	2.3997	0.5229	0.4737	1.5018	0.2123	0.519	0.0067	0.1592	0.247	-0.1218	0.0043	-0.0281	-0.0701	-0.0042	-0.011	0.0457	0.0198	-0.0171	0.0068	-0.0151	0.0822	-7.4158	40.7813	-13.645
11	2.5747	-0.4245	1.1923	2.2589	0.6688	4.1929	0.305	0.6335	0.2777	-0.6	-0.1062	0.0367	-0.0595	-0.0415	-0.1988	0.124	0.0808	0.0449	0.0514	0.1417	-0.009	5.6356	35.3492	-29.8826
12	3.295	-1.1061	0.9565	1.1659	-0.0679	1.4278	-0.1319	-0.212	0.4915	0.0704	0.0431	-0.2368	-0.1354	0.0182	0.0888	0.0181	-0.0121	0.0018	0.0026	-0.0117	0.0941	13.4328	31.7236	-11.0275
13	0.9103	-0.3351	-0.0868	0.6055	0.0879	0.4058	-0.0186	-0.0533	-0.0204	0.006	0.0179	0.0587	0.0058	-0.0063	0.0006	0.0391	-0.0023	-0.0025	0.0461	-0.0101	0.0259	-11.0219	19.2256	-10.3185
14	1.875	-0.9092	-0.3187	2.8968	2.284	5.1783	-0.1233	-0.2089	0.2062	0.03	0.0785	0.0215	-0.2962	0.1051	0.0449	0.0812	0.0038	-0.0033	0.062	-0.0287	0.1181	-20.2753	37.2823	-8.3224

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	4 - 58	5 - 59
2	X-RAY DIFFRACTION	2	A	A	59 - 168	60 - 169
3	X-RAY DIFFRACTION	3	A	A	169 - 226	170 - 227
4	X-RAY DIFFRACTION	4	A	A	227 - 268	228 - 269
5	X-RAY DIFFRACTION	5	A	A	269 - 381	270 - 382
6	X-RAY DIFFRACTION	6	A	A	382 - 420	383 - 421
7	X-RAY DIFFRACTION	7	A	A	421 - 457	422 - 458
8	X-RAY DIFFRACTION	8	B	B	1 - 58	2 - 59
9	X-RAY DIFFRACTION	9	B	B	59 - 134	60 - 135
10	X-RAY DIFFRACTION	10	B	B	135 - 170	136 - 171
11	X-RAY DIFFRACTION	11	B	B	171 - 224	172 - 225
12	X-RAY DIFFRACTION	12	B	B	225 - 268	226 - 269
13	X-RAY DIFFRACTION	13	B	B	269 - 439	270 - 440
14	X-RAY DIFFRACTION	14	B	B	440 - 457	441 - 458

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