PDB-3nc6: CYP134A1 1-phenylimidazole bound structure

ID or keywords:

Entry

Database: PDB / ID: 3nc6

Title

CYP134A1 1-phenylimidazole bound structure

Components

Cytochrome P450 cypX

Keywords

OXIDOREDUCTASE / Cytochrome P450 Oxidase / Haem Protein

Function / homology

Function and homology information

pulcherriminic acid synthase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen / pigment biosynthetic process / iron ion binding / heme binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.1 Å

Authors

Cryle, M.J. / Schlichting, I.

Citation

Journal: Biochemistry / Year: 2010
Title: Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase.
Authors: Cryle, M.J. / Bell, S.G. / Schlichting, I.

History

Deposition	Jun 4, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 11, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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	3nc6.cif.gz	320.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3nc6_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3nc6_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3nc6_validation.xml.gz	31.3 KB	Display
Data in CIF	3nc6_validation.cif.gz	41.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nc/3nc6 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3nc6	HTTPS FTP

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Related structure data

Related structure data	3nc3C 3nc5C 3nc7C C: citing same article (ref.)
Similar structure data	3nc5-2 1a26-d 3nc7-2 3nc5-1 3wec-d 2y5z-2 5y1i-1 2xkr-d 3nc3-1 1gzs-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 (1)

Deposited unit

A: Cytochrome P450 cypX

B: Cytochrome P450 cypX

hetero molecules

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

1

A: Cytochrome P450 cypX

hetero molecules

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

2

B: Cytochrome P450 cypX

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.950, 106.900, 142.930
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	5 - 403
2	1	1	4	B	5 - 403
1	1	2	4	C - A	1 - 406
2	1	2	4	D - B	1 - 406

NCS ensembles :

ID
1
2

#1: Protein	Cytochrome P450 cypX Mass: 49386.129 Da / Num. of mol.: 2 / Mutation: A356T Source method: isolated from a genetically manipulated source Details: pET28a(+) / Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU35060, cyp134, cypB, cypX / Plasmid: Plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O34926, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-PIW / 1-phenyl-1H-imidazole Mass: 144.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₈N₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.72 Å³/Da / Density % sol: 54.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, 0.1 M MgCl2, 12% (w/v) polyethylene glycol-3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.1→48.06 Å / Num. all: 18706 / Num. obs: 18488 / % possible obs: 94.3 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / B_iso Wilson estimate: 72.8 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 12.9
Reflection shell	Resolution: 3.1→3.18 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 4 / Num. unique all: 1340 / % possible all: 86.1

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Processing

Software

Name	Version	Classification
XDS		data scaling
SHARP		phasing
REFMAC	5.5.0070	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.1→43.84 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.879 / SU B: 45.503 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27839	912	4.9 %	RANDOM
R_work	0.21412	-	-	-
obs	0.21733	18488	100 %	-
all	-	18706	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 62.566 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 3.1→43.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6029	0	109	5	6143

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	6281
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.49	2.011	8537
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.485	5	760
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.439	24.014	294
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.571	15	1064
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.406	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	944
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	4783
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.3	1.5	3814
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.586	2	6164
X-RAY DIFFRACTION	r_scbond_it	1.069	3	2467
X-RAY DIFFRACTION	r_scangle_it	1.873	4.5	2372
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	2946	medium positional	0.52	0.5
2	2	43	medium positional	0.27	0.5
1	1	2946	medium thermal	0.49	2
2	2	43	medium thermal	1.12	2

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.323	64	-
R_work	0.229	1260	-
obs	-	1260	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	6.1361	1.1831	0.7804	4.196	0.0755	3.423	-0.0319	0.0356	-0.4811	0.2795	-0.2797	0.5078	0.717	-0.7524	0.3115	0.6375	-0.1658	0.2725	0.9696	-0.0808	0.2337	18.9921	-15.9982	-8.8502
2	3.567	-0.0694	2.7483	9.6384	3.0048	3.45	0.1856	0.2266	-0.2428	-0.2766	0.2543	-0.4705	-0.2028	0.1502	-0.4398	0.2373	0.0682	0.0773	0.5994	0.0144	0.0691	46.4533	-11.0145	-20.1869
3	2.0054	-0.1221	-0.0282	1.6486	1.4418	3.61	0.1096	0.1293	-0.5582	0.1513	-0.1104	0.2149	0.5629	-0.2276	0.0008	0.4028	-0.0117	0.0166	0.618	-0.0245	0.1989	33.4093	-17.3314	-17.9062
4	6.2246	1.0034	0.7701	7.2836	3.5931	5.0004	0.0525	-0.5829	-0.5673	1.1711	-0.3794	1.1498	1.243	-0.8394	0.3269	0.7586	-0.2793	0.2364	0.8269	0.0001	0.2977	23.0773	-13.6452	-0.6439
5	9.0022	1.1705	1.6643	5.4909	0.2163	7.0963	0.1766	-0.0512	0.5687	0.3438	-0.2302	-0.2129	-0.3728	-0.1277	0.0536	0.2575	0.0218	0.0608	0.5516	-0.0165	0.0733	39.1435	-3.2194	-12.5642
6	7.1593	0.038	-0.9605	1.4971	2.3825	4.813	0.1512	-0.3019	0.3508	0.0323	0.1691	-0.5035	-0.1305	0.6313	-0.3202	0.4251	-0.1014	-0.0077	0.8431	0.0681	0.5088	50.6451	11.6638	18.5635
7	0.1069	-0.0465	-0.1242	8.5388	1.2448	4.8669	-0.0615	-0.0637	-0.2488	-1.1103	0.3698	0.1478	0.5978	0.03	-0.3082	0.6697	-0.073	0.0472	0.761	0.0404	0.68	27.7255	-4.4354	21.7263
8	4.669	0.2522	0.8943	3.685	-1.1702	3.7962	-0.0129	-0.4094	0.1152	0.4604	0.3678	0.4523	-0.4506	-0.2709	-0.3548	0.3071	0.0358	0.0722	0.6107	0.0279	0.0736	23.1153	12.5545	32.2909
9	2.9024	0.1918	-0.5767	1.42	-0.4045	3.4355	0.0874	0.0063	-0.4084	-0.0393	0.2026	0.1221	0.1638	-0.1468	-0.29	0.3236	0.0049	-0.027	0.5759	0.0375	0.1074	31.1176	6.5107	26.4935
10	6.363	-0.7311	-0.2596	4.0797	0.1023	3.5795	0.1739	-0.0178	0.3562	-0.5787	0.0935	-0.0249	-0.2876	0.3171	-0.2674	0.3584	-0.0245	0.0617	0.5613	0.0042	0.0436	34.6344	15.164	16.0611

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 102
2	X-RAY DIFFRACTION	2	A	103 - 150
3	X-RAY DIFFRACTION	3	A	151 - 290
4	X-RAY DIFFRACTION	4	A	291 - 353
5	X-RAY DIFFRACTION	5	A	354 - 403
6	X-RAY DIFFRACTION	6	B	4 - 66
7	X-RAY DIFFRACTION	7	B	67 - 104
8	X-RAY DIFFRACTION	8	B	105 - 168
9	X-RAY DIFFRACTION	9	B	169 - 290
10	X-RAY DIFFRACTION	10	B	291 - 404

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