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- PDB-5iut: STRUCTURE OF P450 2B4 F202W MUTANT -

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Basic information

Entry
Database: PDB / ID: 5iut
TitleSTRUCTURE OF P450 2B4 F202W MUTANT
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 2B4 / MONOOXYGENASE / MEMBRANE PROTEIN
Function / homology
Function and homology information


arachidonate epoxygenase activity / epoxygenase P450 pathway / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2B-like / : / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 ...Cytochrome P450, E-class, group I, CYP2B-like / : / Cytochrome P450, E-class, group I / 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
3,6,9,12,15,18-hexaoxahexacosan-1-ol / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsJang, H.-H. / Halpert, J.R. / Shah, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES003619 United States
CitationJournal: Biophys.Chem. / Year: 2016
Title: Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry.
Authors: Shah, M.B. / Jang, H.H. / Wilderman, P.R. / Lee, D. / Li, S. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4953
Polymers54,4841
Non-polymers1,0112
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.165, 91.165, 151.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytochrome P450 2B4 / CYPIIB4 / Cytochrome P450 isozyme 2 / Cytochrome P450 LM2 / Cytochrome P450 type B0 / Cytochrome P450 type B1


Mass: 54484.406 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-491 / Mutation: F202W, P221S, H226Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2B4 / Plasmid: PKK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P00178, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-32M / 3,6,9,12,15,18-hexaoxahexacosan-1-ol / HEXAETHYLENE GLYCOL MONOOCTYL ETHER


Mass: 394.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS INDICATE THAT THERE IS AN ERROR IN THE SEQUENCE DATABASE REFERENCE AT RESIDUE 221

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 4000, 0.1M CITRATE, 10% 2- PROPANOL, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 25, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.33→39.03 Å / Num. obs: 30766 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.3
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4 / % possible all: 70.4

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Processing

Software
NameVersionClassification
autoXDSdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0072refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVR

3mvr


Resolution: 2.34→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.468 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.235 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1537 5 %RANDOM
Rwork0.216 ---
obs0.218 28912 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 39.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.34→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 70 179 3900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223824
X-RAY DIFFRACTIONr_bond_other_d0.0030.022665
X-RAY DIFFRACTIONr_angle_refined_deg1.0092.0065191
X-RAY DIFFRACTIONr_angle_other_deg1.0273.0056434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1915457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97922.712177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20915608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5611534
X-RAY DIFFRACTIONr_chiral_restr0.0550.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02825
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_it0.4721.52297
X-RAY DIFFRACTIONr_mcbond_other0.0541.5919
X-RAY DIFFRACTIONr_mcangle_it0.89523720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96931527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7334.51471
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 81 -
Rwork0.394 1568 -
obs--72.71 %

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