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- PDB-3lxh: Crystal Structure of Cytochrome P450 CYP101D1 -

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Basic information

Entry
Database: PDB / ID: 3lxh
TitleCrystal Structure of Cytochrome P450 CYP101D1
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 fold / Heme / Iron / Metal-binding / Monooxygenase
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
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Cytochrome P450
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, W. / Bell, S.G. / Wang, H. / Bartlam, M. / Wong, L.L. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Molecular characterization of a class I P450 electron transfer system from Novosphingobium aromaticivorans DSM12444
Authors: Yang, W. / Bell, S.G. / Wang, H. / Zhou, W. / Hoskins, N. / Dale, A. / Bartlam, M. / Wong, L.L. / Rao, Z.
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,56711
Polymers94,6762
Non-polymers1,8919
Water8,377465
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4227
Polymers47,3381
Non-polymers1,0846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1444
Polymers47,3381
Non-polymers8063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.902, 150.902, 195.318
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Cytochrome P450 / 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: DSM 12444 / Gene: Saro_0514 / Plasmid: pET28a / 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-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1M Tris, pH 8.2, 12% 1,4-dioxane, 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 67017 / Num. obs: 66042 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / Num. unique all: 6580 / % possible all: 86.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 2.2→49.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.115 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.203 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23988 3332 5.1 %RANDOM
Rwork0.19964 ---
obs0.20166 62622 98.53 %-
all-63556 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å2-0 Å2
2--0.98 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6453 0 122 465 7040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226747
X-RAY DIFFRACTIONr_angle_refined_deg1.7842.0129199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29622.675314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.389151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4511568
X-RAY DIFFRACTIONr_chiral_restr0.1570.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215198
X-RAY DIFFRACTIONr_mcbond_it0.7291.54061
X-RAY DIFFRACTIONr_mcangle_it1.41226580
X-RAY DIFFRACTIONr_scbond_it2.53132686
X-RAY DIFFRACTIONr_scangle_it4.0624.52619
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 191 -
Rwork0.264 3910 -
obs--84.11 %

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