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- PDB-3ofu: Crystal Structure of Cytochrome P450 CYP101C1 -

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Basic information

Entry
Database: PDB / ID: 3ofu
TitleCrystal Structure of Cytochrome P450 CYP101C1
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE
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
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-ID3 / Cytochrome P450
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhou, W. / Ma, M. / Bell, S.G. / Yang, W. / Hao, Y. / Rees, N.H. / Bartlam, M. / Wong, L.-L. / Rao, Z.
CitationJournal: Chembiochem / Year: 2011
Title: Structural Analysis of CYP101C1 from Novosphingobium aromaticivorans DSM12444.
Authors: Ma, M. / Bell, S.G. / Yang, W. / Hao, Y. / Rees, N.H. / Bartlam, M. / Zhou, W. / Wong, L.L. / Rao, Z.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Cytochrome P450
C: Cytochrome P450
D: Cytochrome P450
E: Cytochrome P450
F: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,48415
Polymers262,2096
Non-polymers4,2769
Water5,585310
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5103
Polymers43,7011
Non-polymers8092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5103
Polymers43,7011
Non-polymers8092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5103
Polymers43,7011
Non-polymers8092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3182
Polymers43,7011
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3182
Polymers43,7011
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3182
Polymers43,7011
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 113.418, 150.234
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytochrome P450 / CYP101C1


Mass: 43701.445 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_2249 / Plasmid: pET28a / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): BL21(DE3) / References: UniProt: Q2G637
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ID3 / (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one / beta-ionone


Mass: 192.297 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H20O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Bis-Tris, pH 5.0, 30% w/v polyethylene glycol monomethyl ether 2000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→150.76 Å / Num. all: 55970 / Num. obs: 53086 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 27.444 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.116 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.78 / Num. unique all: 5614 / Rsym value: 0.409 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H7R

2h7r


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.848 / SU B: 19.253 / SU ML: 0.383 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.517 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30263 2829 5.1 %RANDOM
Rwork0.19257 ---
obs0.19824 53086 95 %-
all-55916 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.444 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.76 Å2
2--0.96 Å20 Å2
3----0.78 Å2
Refine analyzeLuzzati coordinate error obs: 0.3368 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18307 0 300 310 18917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.02219075
X-RAY DIFFRACTIONr_angle_refined_deg2.52.01526014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08252353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45822.521829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.875153059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.68815202
X-RAY DIFFRACTIONr_chiral_restr0.160.22833
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02114694
X-RAY DIFFRACTIONr_mcbond_it1.1641.511782
X-RAY DIFFRACTIONr_mcangle_it1.998218948
X-RAY DIFFRACTIONr_scbond_it3.29237293
X-RAY DIFFRACTIONr_scangle_it4.8784.57066
LS refinement shellResolution: 2.798→2.871 Å / Rfactor Rfree error: 0.0507 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.505 191 -
Rwork0.277 3896 -
obs-3896 97.33 %

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