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- PDB-3nc7: CYP134A1 2-phenylimidazole bound structure -

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Basic information

Entry
Database: PDB / ID: 3nc7
TitleCYP134A1 2-phenylimidazole bound structure
ComponentsCytochrome P450 cypX
KeywordsOXIDOREDUCTASE / 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
Cytochrome P450, CypX / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 2-phenyl-1H-imidazole / Pulcherriminic acid synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsCryle, M.J. / Schlichting, I.
CitationJournal: 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
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 cypX
B: Cytochrome P450 cypX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3428
Polymers98,7722
Non-polymers1,5706
Water362
1
A: Cytochrome P450 cypX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1714
Polymers49,3861
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 cypX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1714
Polymers49,3861
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.360, 106.790, 142.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A4 - 404
2114B4 - 404
1124C - A1 - 406
2124D - B1 - 406

NCS ensembles :
ID
1
2

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Components

#1: Protein Cytochrome P450 cypX


Mass: 49386.129 Da / Num. of mol.: 2 / Mutation: A356T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU35060, cyp134, cypB, cypX / Plasmid: pET28a(+) / 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PIY / 2-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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→47.67 Å / Num. all: 15331 / Num. obs: 15206 / % possible obs: 95.8 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.4
Reflection shellResolution: 3.3→3.385 Å / Redundancy: 5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1290 / % possible all: 89.4

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.3→43.55 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.85 / SU B: 58.921 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.626 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28613 751 4.9 %RANDOM
Rwork0.21094 ---
obs0.21473 15206 100 %-
all-15331 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.113 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 3.3→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 110 2 6133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2532.0128523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9255759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35324.061293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.802151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3691545
X-RAY DIFFRACTIONr_chiral_restr0.0850.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214777
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2321.53815
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46826167
X-RAY DIFFRACTIONr_scbond_it0.7832455
X-RAY DIFFRACTIONr_scangle_it1.4094.52355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12982MEDIUM POSITIONAL0.660.5
12982MEDIUM THERMAL0.32
243MEDIUM POSITIONAL0.360.5
243MEDIUM THERMAL0.62
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 56 -
Rwork0.241 1047 -
obs-1047 100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.6722-1.18562.14879.1505-0.51484.0745-0.36190.08990.17210.1220.16481.03120.4201-1.35150.1970.2628-0.11320.09830.8515-0.1580.265113.3781-10.2119-7.4582
25.17864.7089-2.37186.86710.01592.93880.08090.2247-0.33840.1923-0.3114-0.03330.0684-0.53420.23050.75680.00870.1110.69230.15360.822831.7932-27.2083-12.789
33.78490.18171.20863.10412.16313.06360.17620.4514-0.1396-0.3744-0.0397-0.07290.08870.0342-0.13640.16580.06040.00970.35320.04030.020938.3086-16.1711-25.7741
43.3257-0.1463-0.54244.15492.23063.5094-0.03060.0189-0.52450.1828-0.13090.21460.5538-0.24730.16150.2261-0.01150.02610.24020.01840.096532.3134-15.0218-9.9718
56.440.2995-1.3224.99240.46334.67070.1486-0.1237-0.05140.5516-0.16920.18380.2634-0.25210.02060.1291-0.00830.02790.1637-0.01480.010731.9124-8.0631-6.1811
64.8072-0.1381-0.64731.480.453.93520.0361-0.191-0.19130.1503-0.0488-0.17770.06760.53540.01260.2843-0.01140.03570.4948-0.03450.056946.07878.154819.1412
76.498-2.99591.63524.1494-1.15024.44340.0011-0.28020.31020.16510.14960.0101-0.0418-0.3623-0.15080.17860.01730.0270.2333-0.0270.040621.832211.864431.3775
82.28010.5259-0.65581.5408-0.33233.83270.1565-0.1517-0.2157-0.09220.05430.02570.08880.0015-0.21080.071-0.0115-0.02530.2208-0.0020.046930.89326.561326.2923
96.2614-0.3094-0.34433.56120.13253.07690.12420.03910.1959-0.48940.0103-0.0845-0.23830.3234-0.13460.1515-0.00730.03850.19480.01110.018534.770114.083114.2204
108.2478-6.9519-2.05136.26963.46128.0298-0.4428-0.7823-0.16070.35360.85290.0535-0.07220.6877-0.41010.2373-0.06170.13080.3360.06250.182231.539521.666725.851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 57
2X-RAY DIFFRACTION2A58 - 107
3X-RAY DIFFRACTION3A108 - 200
4X-RAY DIFFRACTION4A201 - 296
5X-RAY DIFFRACTION5A297 - 403
6X-RAY DIFFRACTION6B6 - 101
7X-RAY DIFFRACTION7B102 - 167
8X-RAY DIFFRACTION8B168 - 290
9X-RAY DIFFRACTION9B291 - 391
10X-RAY DIFFRACTION10B392 - 404

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