PDB-4c9k: Structure of Camphor and Hydroxycamphor bound wild type CYP101D1

ID or keywords:

Entry

Database: PDB / ID: 4c9k

Title

Structure of Camphor and Hydroxycamphor bound wild type CYP101D1

Components

CYTOCHROME P450

Keywords

OXIDOREDUCTASE / MONO-OXYGENASE

Function / homology

Function and homology information

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / membrane
Similarity search - Function

Biological species

NOVOSPHINGOBIUM AROMATICIVORANS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 Å

Authors

Batabyal, D. / L Poulos, T.

Citation

Journal: Biochemistry / Year: 2013
Title: Crystal Structures and Functional Characterization of Wild-Type Cyp101D1 and its Active Site Mutants.
Authors: Batabyal, D. / Poulos, T.L.

History

Deposition	Oct 2, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 19, 2014	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_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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PDBx/mmCIF format	4c9k.cif.gz	344.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4c9k.ent.gz	281.8 KB	Display	PDB format
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Validation report

Summary document	4c9k_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4c9k_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4c9k_validation.xml.gz	36.4 KB	Display
Data in CIF	4c9k_validation.cif.gz	53.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/4c9k ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c9k	HTTPS FTP

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Related structure data

Related structure data	4c9lC 4c9mC 4c9nC 4c9oC 4c9pC 3lxiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3lxh-2 4c9o-1 4c9o-2 4c9m-1 4c9p-1 6wgw-2 4c9n-2 3lxi-2 6gk6-d 3lxi-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	#82 - Oct 2006 Cytochrome p450 similarity (3)

Deposited unit

A: CYTOCHROME P450

B: CYTOCHROME P450

hetero molecules

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

1

A: CYTOCHROME P450

hetero molecules

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

2

B: CYTOCHROME P450

hetero molecules

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

Unit cell

Length a, b, c (Å)	151.318, 151.318, 196.141
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

#1: Protein	CYTOCHROME P450 / CYP101D1 Mass: 47337.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOVOSPHINGOBIUM AROMATICIVORANS (bacteria) Strain: DSM12444 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GB12
#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-CAH / 5-EXO-HYDROXYCAMPHOR Mass: 168.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆O₂
#4: Chemical	ChemComp-CAM / CAMPHOR Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆O
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 543 / 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: 3.42 Å³/Da / Density % sol: 64.07 % / Description: NONE
Crystal grow	pH: 8.2 / Details: 100MM TRIS PH 8.2, 1.6M AMMONIUM SULPHATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.18→50.2 Å / Num. obs: 69832 / % possible obs: 99.9 % / Observed criterion σ(I): 7 / Redundancy: 14.2 % / B_iso Wilson estimate: 30.87 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 28.4
Reflection shell	Resolution: 2.18→2.3 Å / Redundancy: 14.3 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 7 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LXI

3lxi

Resolution: 2.18→49.53 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 20.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2181	3459	5 %
R_work	0.1753	-	-
obs	0.1775	68585	98.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.18→49.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6471	0	132	543	7146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6800
X-RAY DIFFRACTION	f_angle_d	1.155	9292
X-RAY DIFFRACTION	f_dihedral_angle_d	14.302	2528
X-RAY DIFFRACTION	f_chiral_restr	0.079	1001
X-RAY DIFFRACTION	f_plane_restr	0.004	1209

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 (%)
2.18-2.2099	0.2269	129	0.1841	2559	X-RAY DIFFRACTION	98
2.2099-2.2415	0.2304	146	0.1797	2559	X-RAY DIFFRACTION	100
2.2415-2.2749	0.2219	137	0.1852	2585	X-RAY DIFFRACTION	100
2.2749-2.3105	0.2342	152	0.1777	2586	X-RAY DIFFRACTION	100
2.3105-2.3483	0.2168	122	0.1755	2589	X-RAY DIFFRACTION	100
2.3483-2.3888	0.2453	150	0.175	2584	X-RAY DIFFRACTION	100
2.3888-2.4323	0.2299	144	0.1746	2575	X-RAY DIFFRACTION	100
2.4323-2.479	0.2235	146	0.1744	2605	X-RAY DIFFRACTION	100
2.479-2.5296	0.2185	127	0.1818	2588	X-RAY DIFFRACTION	100
2.5296-2.5846	0.2214	133	0.1805	2610	X-RAY DIFFRACTION	100
2.5846-2.6448	0.2559	154	0.1825	2575	X-RAY DIFFRACTION	100
2.6448-2.7109	0.2108	131	0.1796	2570	X-RAY DIFFRACTION	98
2.7109-2.7842	0.2458	130	0.1982	2509	X-RAY DIFFRACTION	96
2.7842-2.8661	0.3059	150	0.2034	2516	X-RAY DIFFRACTION	97
2.8661-2.9586	0.2511	135	0.1992	2548	X-RAY DIFFRACTION	97
2.9586-3.0643	0.2621	136	0.1965	2537	X-RAY DIFFRACTION	97
3.0643-3.187	0.222	143	0.1954	2569	X-RAY DIFFRACTION	98
3.187-3.332	0.245	142	0.1849	2566	X-RAY DIFFRACTION	98
3.332-3.5077	0.2261	137	0.1712	2602	X-RAY DIFFRACTION	98
3.5077-3.7274	0.2306	133	0.1634	2603	X-RAY DIFFRACTION	98
3.7274-4.015	0.1935	144	0.1608	2631	X-RAY DIFFRACTION	99
4.015-4.4189	0.178	134	0.1461	2683	X-RAY DIFFRACTION	100
4.4189-5.0577	0.1633	123	0.1466	2724	X-RAY DIFFRACTION	100
5.0577-6.3701	0.202	143	0.1874	2733	X-RAY DIFFRACTION	100
6.3701-49.5432	0.2003	138	0.1837	2920	X-RAY DIFFRACTION	100

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	0.9977	-0.8986	-0.0848	1.6552	0.0551	0.7145	-0.0029	0.0558	0.0659	-0.1543	0.0264	-0.1302	-0.059	0.1023	-0.0256	0.1375	-0.0286	-0.0132	0.2373	-0.0261	0.1417	34.8966	17.5187	3.9519
2	1.3828	0.3161	-0.1792	0.9418	0.4528	1.3327	-0.0416	0.0503	0.0419	-0.289	0.0371	0.283	-0.1262	-0.1393	0.0018	0.2541	0.0298	-0.096	0.2194	0.022	0.2025	11.1969	30.4398	3.2587
3	1.6125	0.3502	0.2773	3.6811	0.1506	2.159	-0.0916	0.192	0.3018	-0.2317	0.1556	-0.1511	-0.3537	0.2898	-0.0816	0.2954	-0.0529	-0.0203	0.2503	0.0389	0.2072	27.43	39.0408	-5.4925
4	1.6064	-0.2587	-0.2958	1.0012	0.0257	1.0073	-0.1023	-0.155	-0.0331	0.0381	0.0792	0.057	-0.0869	0.006	0.0156	0.1456	0.0023	-0.037	0.1931	-0.0101	0.1228	25.3148	21.2559	13.0435
5	1.6818	-0.2735	-0.2318	2.0529	0.5922	2.2364	-0.0559	-0.0611	-0.2278	0.0241	-0.0401	0.4035	-0.0034	-0.3255	0.0808	0.1171	0.0138	-0.0526	0.2211	0.0345	0.2165	8.0856	20.4505	10.6044
6	1.8915	-1.0077	-0.0248	1.8035	0.1516	1.0448	-0.0243	-0.3075	0.1006	0.1084	0.0798	0.1102	0.0179	0.0309	-0.0578	0.112	0.0215	0.0032	0.3065	-0.0257	0.1648	39.2675	17.0923	38.284
7	1.931	-0.5472	-0.1906	1.7608	-0.2846	0.5769	-0.0213	0.0556	0.2012	-0.1091	-0.0484	-0.2905	-0.0184	0.1023	0.0713	0.1298	0.0172	0.0113	0.3507	0.0171	0.2635	62.6133	11.1322	27.276
8	1.0592	1.0732	-0.3682	1.4053	-0.0231	1.1148	-0.0296	-0.422	-0.3011	0.0968	-0.0962	-0.3415	0.225	0.2232	0.1278	0.1549	0.078	0.017	0.3249	0.0582	0.3202	65.6254	-2.4653	37.8385
9	3.3013	-0.2278	-0.3464	1.4375	0.103	2.4252	-0.0117	-0.3924	0.3253	0.0812	-0.0342	-0.3262	-0.1649	0.1472	0.0436	0.1667	-0.0043	-0.0687	0.3598	-0.0074	0.3651	66.5942	18.522	35.9539
10	2.1307	-0.8882	0.054	2.5905	-0.2117	0.9326	0.0072	0.0788	-0.2318	-0.1776	-0.0127	0.1202	0.1017	-0.0484	0.0105	0.109	0.0063	0.0002	0.2406	0.0104	0.1641	45.3298	4.9966	28.8456
11	2.128	-0.6496	-0.1967	2.2314	0.7078	2.1859	-0.1132	-0.1254	-0.582	0.2214	0.0517	0.0611	0.4282	0.0974	0.0709	0.1562	0.0566	0.0176	0.2682	0.0627	0.3458	55.4799	-6.947	37.1029

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 10 THROUGH 122 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 123 THROUGH 193 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 194 THROUGH 242 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 243 THROUGH 367 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 368 THROUGH 417 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 11 THROUGH 91 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 92 THROUGH 145 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 146 THROUGH 172 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 173 THROUGH 259 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 260 THROUGH 367 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 368 THROUGH 417 )

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