PDB-4c9o: Structure of Cyanide and Camphor bound D259N mutant of CYP101D1

ID or keywords:

Entry

Database: PDB / ID: 4c9o

Title

Structure of Cyanide and Camphor bound D259N mutant of CYP101D1

Components

CYTOCHROME P450

Keywords

OXIDOREDUCTASE / MONO-OXYGENASE / P450

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: 1.977 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	Dec 25, 2013	Group: Atomic model / Other
Revision 1.2	Feb 19, 2014	Group: Database references
Revision 1.3	Sep 23, 2015	Group: Data collection
Revision 1.4	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 / 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 / _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	4c9o.cif.gz	486.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4c9o.ent.gz	408.1 KB	Display	PDB format
PDBx/mmJSON format	4c9o.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4c9o_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4c9o_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4c9o_validation.xml.gz	41.2 KB	Display
Data in CIF	4c9o_validation.cif.gz	64 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/4c9o ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c9o	HTTPS FTP

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Related structure data

Related structure data	4c9kC 4c9lC 4c9mC 4c9nC 4c9pC 3lxiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4c9k-1 4c9m-1 4c9p-1 3lxi-1 3lxh-2 6wgw-2 5mns-4 4c9k-2 3tyw-4 3ofu-2 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 (2) #111 - Mar 2009 Hydrogenase similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: CYTOCHROME P450

B: CYTOCHROME P450

hetero molecules

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

1

A: CYTOCHROME P450

hetero molecules

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

2

B: CYTOCHROME P450

hetero molecules

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

Unit cell

Length a, b, c (Å)	152.377, 152.377, 197.426
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

Components on special symmetry positions

ID	Model	Components
1	1	A-2020- HOH
2	1	A-2135- HOH

#1: Protein	CYTOCHROME P450 / CYP101D1 Mass: 47336.988 Da / Num. of mol.: 2 / Mutation: YES 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-CAM / CAMPHOR Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆O
#4: Chemical	ChemComp-CYN / CYANIDE ION Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1010 / 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: 3.49 Å³/Da / Density % sol: 64.8 % / 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	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: 1.98→50 Å / Num. obs: 94411 / % possible obs: 99.9 % / Observed criterion σ(I): 5.1 / Redundancy: 14.5 % / B_iso Wilson estimate: 23.85 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 24
Reflection shell	Resolution: 1.98→2.09 Å / Redundancy: 14.4 % / R_merge(I) obs: 0.61 / Mean I/σ(I) obs: 5.1 / % possible all: 99.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LXI

3lxi

Resolution: 1.977→49.802 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 15.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1817	4729	5 %
R_work	0.1471	-	-
obs	0.1489	94318	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.977→49.802 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6471	0	112	1010	7593

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6783
X-RAY DIFFRACTION	f_angle_d	1.373	9260
X-RAY DIFFRACTION	f_dihedral_angle_d	14.62	2530
X-RAY DIFFRACTION	f_chiral_restr	0.09	995
X-RAY DIFFRACTION	f_plane_restr	0.006	1206

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 (%)
1.9768-1.9993	0.2123	164	0.1723	2812	X-RAY DIFFRACTION	96
1.9993-2.0228	0.2273	150	0.1629	2921	X-RAY DIFFRACTION	100
2.0228-2.0475	0.1813	142	0.1604	2969	X-RAY DIFFRACTION	100
2.0475-2.0734	0.213	171	0.1565	2941	X-RAY DIFFRACTION	100
2.0734-2.1007	0.2003	150	0.1543	2940	X-RAY DIFFRACTION	100
2.1007-2.1295	0.2061	154	0.1467	2958	X-RAY DIFFRACTION	100
2.1295-2.1599	0.1847	162	0.1397	2934	X-RAY DIFFRACTION	100
2.1599-2.1921	0.1772	166	0.136	2941	X-RAY DIFFRACTION	100
2.1921-2.2264	0.1603	141	0.133	2970	X-RAY DIFFRACTION	100
2.2264-2.2629	0.1791	154	0.1332	2946	X-RAY DIFFRACTION	100
2.2629-2.3019	0.1784	149	0.1352	2964	X-RAY DIFFRACTION	100
2.3019-2.3438	0.1901	153	0.1352	2971	X-RAY DIFFRACTION	100
2.3438-2.3888	0.1694	150	0.1293	2983	X-RAY DIFFRACTION	100
2.3888-2.4376	0.1562	167	0.1321	2927	X-RAY DIFFRACTION	100
2.4376-2.4906	0.192	157	0.1324	2971	X-RAY DIFFRACTION	100
2.4906-2.5485	0.1854	139	0.1395	2985	X-RAY DIFFRACTION	100
2.5485-2.6123	0.1712	141	0.1425	2993	X-RAY DIFFRACTION	100
2.6123-2.6829	0.178	147	0.1469	2979	X-RAY DIFFRACTION	100
2.6829-2.7618	0.2166	175	0.1531	2956	X-RAY DIFFRACTION	100
2.7618-2.851	0.2086	162	0.1508	2972	X-RAY DIFFRACTION	100
2.851-2.9528	0.1825	174	0.1532	2979	X-RAY DIFFRACTION	100
2.9528-3.0711	0.1863	156	0.1546	2991	X-RAY DIFFRACTION	100
3.0711-3.2108	0.1922	160	0.1505	3002	X-RAY DIFFRACTION	100
3.2108-3.38	0.1925	178	0.1475	2997	X-RAY DIFFRACTION	100
3.38-3.5918	0.1615	149	0.1426	3028	X-RAY DIFFRACTION	100
3.5918-3.869	0.1596	157	0.135	3029	X-RAY DIFFRACTION	100
3.869-4.2581	0.1469	149	0.1257	3061	X-RAY DIFFRACTION	100
4.2581-4.8739	0.1635	164	0.1221	3068	X-RAY DIFFRACTION	100
4.8739-6.1388	0.1908	179	0.1644	3109	X-RAY DIFFRACTION	100
6.1388-49.8182	0.1976	169	0.2036	3292	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	0.0146	-0.0192	0.0115	0.039	-0.0089	0.0097	-0.027	0.0467	-0.0965	-0.0484	0.0223	0.0585	0.0605	0.0096	-0.0085	0.0736	-0.0045	-0.0103	0.1285	-0.0214	0.1007	33.1338	6.6838	2.7934
2	0.0604	-0.0659	0.0189	0.0971	-0.0062	0.0991	-0.0021	0.0544	0.0449	-0.086	0.018	-0.0279	-0.1292	0.0233	0.0816	0.036	-0.0028	-0.0377	0.1172	-0.01	0.0564	24.0113	29.8254	6.1127
3	0.0718	-0.029	0.0316	0.0406	-0.0456	0.0511	0.0096	0.1733	0.0112	-0.0705	-0.0043	0.032	-0.0395	0.1016	0.0001	0.1442	-0.0304	-0.0257	0.1616	0.0215	0.1179	25.818	35.271	-5.67
4	0.064	-0.0253	0.0538	0.1685	0.0093	0.059	-0.0512	-0.1005	-0.0401	0.0465	0.057	-0.0002	-0.0296	0.0361	0.0218	0.0533	0.0164	-0.0096	0.1311	0.0046	0.0639	25.1849	19.5277	15.0483
5	0.0077	-0.0002	-0.01	0.0912	-0.0273	0.0533	-0.0413	-0.0004	-0.1326	0.015	0.059	0.0971	-0.0183	-0.0914	0.0457	0.0202	0.013	-0.0215	0.1379	0.0055	0.1247	8.25	20.5982	10.5686
6	0.0211	0.007	-0.0164	0.1156	0.0081	0.0206	-0.0247	-0.1479	0.0432	-0.0124	0.0282	0.035	0.0207	0.0488	0.009	0.0612	0.0367	0.0086	0.1892	-0.001	0.0875	39.5494	17.1455	38.4164
7	0.1375	0.0238	0.0319	0.0198	0.0151	0.0273	-0.0382	-0.0671	0.0267	-0.0118	0.0328	-0.0647	-0.0119	0.0694	-0.0253	0.0736	0.042	0.02	0.2223	0.0182	0.1587	63.9718	6.6816	30.8559
8	0.0205	0.0195	0.0093	0.1704	-0.0413	0.0226	-0.0455	-0.2284	0.1946	0.0445	-0.0438	-0.1288	-0.0618	-0.026	-0.0936	-0.0571	0.0094	-0.0406	0.2966	-0.0096	0.1743	66.9218	18.7878	36.2385
9	0.1453	0.0446	-0.0026	0.0222	-0.0089	0.0821	0.0042	0.0134	-0.0927	-0.0266	-0.0137	0.0749	-0.0032	-0.0206	-0.005	0.0417	0.0139	-0.0056	0.1246	0.0046	0.1232	45.9374	5.0333	29.1704
10	0.1298	0.0243	0.0337	0.0343	0.0346	0.0236	-0.0554	-0.0523	-0.2714	0.0752	0.0296	0.0526	0.0263	-0.0014	0.011	0.0782	0.0676	0.0353	0.1767	0.0549	0.2078	55.8392	-6.9753	37.2929

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 10 THROUGH 63 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 64 THROUGH 172 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 173 THROUGH 257 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 258 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 172 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 173 THROUGH 257 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 258 THROUGH 367 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 368 THROUGH 417 )

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