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- PDB-2bdm: Structure of Cytochrome P450 2B4 with Bound Bifonazole -

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Basic information

Entry
Database: PDB / ID: 2bdm
TitleStructure of Cytochrome P450 2B4 with Bound Bifonazole
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / p450 / Monooxygenase / membrane protein / CYP 2B4 / CYP LM2
Function / homology
Function and homology information


arachidonic acid epoxygenase activity / epoxygenase P450 pathway / unspecific monooxygenase / aromatase activity / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhao, Y. / White, M.A. / Muralidhara, B.K. / Sun, L. / Halpert, J.R. / Stout, C.D.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.
Authors: Zhao, Y. / White, M.A. / Muralidhara, B.K. / Sun, L. / Halpert, J.R. / Stout, C.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: An open conformation of mammalian cytochrome P450 2B4 at 1.6-resolution
Authors: Scott, E.E. / He, Y.A. / Wester, M.R. / White, M.A. / Chin, C.C. / Halpert, J.R. / Johnson, E.F. / Stout, C.D.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding
Authors: Scott, E.E. / White, M.A. / He, Y.A. / Johnson, E.F. / D Stout, C. / Halpert, J.R.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Authors indicate that there is an error in the sequence database reference at residue 221.

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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)57,6959
Polymers54,1691
Non-polymers3,5268
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome P450 2B4
hetero molecules

A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,39018
Polymers108,3382
Non-polymers7,05216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area24560 Å2
ΔGint-169 kcal/mol
Surface area36870 Å2
MethodPISA, PQS
3
A: Cytochrome P450 2B4
hetero molecules

A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,39018
Polymers108,3382
Non-polymers7,05216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area13230 Å2
ΔGint-104 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.210, 203.210, 103.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

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Components

#1: Protein Cytochrome P450 2B4 / CYPIIB4 / P450-LM2 / Isozyme 2 / P450 types B0 and B1


Mass: 54169.082 Da / Num. of mol.: 1 / Fragment: residues 28-491
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-TMI / 1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE / BIFONAZOLE


Mass: 310.392 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H18N2 / Comment: antifungal*YM
#4: Chemical
ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 5.35 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NaCl, pH 6.5, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→28.54 Å / Num. obs: 56020 / % possible obs: 99.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.3-2.361008.50.4671.640670.467
2.36-2.421009.90.4271.839810.427
2.42-2.4910010.20.381238630.381
2.49-2.5710010.30.3282.337710.328
2.57-2.6610010.40.2852.736550.285
2.66-2.7510010.50.2353.235430.235
2.75-2.8510010.50.2073.734170.207
2.85-2.9710010.50.1684.533080.168
2.97-3.110010.50.1385.431430.138
3.1-3.2510010.50.1027.230580.102
3.25-3.4310010.50.0828.728870.082
3.43-3.6410010.40.0689.827520.068
3.64-3.8910010.40.05910.725830.059
3.89-4.210010.30.05411.524210.054
4.2-4.610010.10.04912.122500.049
4.6-5.14100100.04612.720330.046
5.14-5.941009.40.04114.618200.041
5.94-7.2799.590.03218.515470.032
7.27-10.2999.910.10.02424.312420.024
10.29-28.5493.38.40.028216790.028

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PO5, 1SUO

1po5

1suo


Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2750 4.9 %random selection
Rwork0.196 ---
all0.2 55929 --
obs0.2 55929 100 %-
Solvent computationBsol: 56.706 Å2
Displacement parametersBiso mean: 63.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.153 Å2-2.294 Å20 Å2
2--0.153 Å20 Å2
3----0.306 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 251 131 4116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.297
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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