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- PDB-3kw4: Crystal structure of cytochrome 2B4 in complex with the anti-plat... -

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Basic information

Entry
Database: PDB / ID: 3kw4
TitleCrystal structure of cytochrome 2B4 in complex with the anti-platelet drug ticlopidine
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / P450 / cytochrome P450 2B4 / monooxygenase / membrane protein / CYP 2B4 / CYP LM2 / Endoplasmic reticulum / Heme / Iron / Membrane / Metal-binding / Microsome
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 ...: / 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
Chem-CH0 / PROTOPORPHYRIN IX CONTAINING FE / ticlopidine / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 Å
AuthorsGay, S.C. / Maekawa, K. / Roberts, A.G. / Hong, W.-X. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
Citation
Journal: Biochemistry / Year: 2010
Title: Structures of cytochrome P450 2B4 complexed with the antiplatelet drugs ticlopidine and clopidogrel.
Authors: Gay, S.C. / Roberts, A.G. / Maekawa, K. / Talakad, J.C. / Hong, W.X. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 {angstrom} resolution: Insight into the range of P450 conformations and coordination of redox partner binding.
Authors: Scott, E.E. / White, M.A. / He, Y.A. / Johnson, E.F. / Stout, C.D. / Halpert, J.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: An open conformation of mammalian cytochrome P450 2B4 at 1.6 A 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.
#4: Journal: Biochemistry / Year: 2007
Title: Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
Authors: Zhao, Y. / Sun, L. / Muralidhara, B.K. / White, M.A. / Stout, C.D. / Halpert, J.R.
#5: Journal: Biochemistry / Year: 2009
Title: Crystal Structures of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-methyl-1H-imidazole: Ligand-Induced Structural Response through Alpha-Helical Repositioning
Authors: Gay, S.C. / Sun, L. / Maekawa, K. / Halpert, J.R. / Stout, C.D.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Atomic model
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)57,5226
Polymers54,1691
Non-polymers3,3535
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 93.500, 137.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 54169.082 Da / Num. of mol.: 1
Mutation: E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, H226Y
Source method: isolated from a genetically manipulated source
Details: Deleted residues 3-21, E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, 4x Cterm His tag
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

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Non-polymers , 5 types, 36 molecules

#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-TIC / ticlopidine / 5-(2-chlorobenzyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridine


Mass: 263.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14ClNS / Comment: medication, inhibitor*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.: 2 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#5: Chemical ChemComp-CH0 / 2-{[(3alpha,5alpha,7alpha,8alpha,10alpha,12alpha,17alpha)-3,12-bis{2-[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]ethoxy}cholan-7-yl]oxy}ethyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside / 3,7,12-tris[(-D-maltopyranosyl)ethyloxy]cholane


Mass: 1483.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C66H114O36
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 20% (w/v) PEG 8000, 0.2 M MgCl2 and 0.1 M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 4.2 / Number: 173539 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / D res high: 2.5 Å / D res low: 80.973 Å / Num. obs: 24553 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.9169.7294.710.0570.0576
5.597.9110010.0740.0747
4.565.5910010.090.097.2
3.954.5610010.0870.0877.2
3.543.9510010.1530.1537.1
3.233.5410010.1770.1777.2
2.993.2310010.1840.1847.3
2.82.9910010.2830.2837.3
2.642.810010.5050.5057
2.52.6410010.6950.6956.7
ReflectionResolution: 2.67→80.973 Å / Num. obs: 20223 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 4.9
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.416 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å69.72 Å
Translation2.5 Å69.72 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SUO

1suo


Resolution: 2.67→68.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.152 / SU ML: 0.253 / SU R Cruickshank DPI: 0.407 / Cross valid method: THROUGHOUT / ESU R: 0.626 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1028 5.1 %RANDOM
Rwork0.195 ---
obs0.198 19135 99.6 %-
all-24605 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.735 Å20 Å20 Å2
2---5.735 Å20 Å2
3---11.47 Å2
Refinement stepCycle: LAST / Resolution: 2.67→68.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 208 31 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4062.0495438
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8422.644174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07415627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8941533
X-RAY DIFFRACTIONr_chiral_restr0.0840.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222983
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_it0.8971.52326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73623767
X-RAY DIFFRACTIONr_scbond_it2.55431667
X-RAY DIFFRACTIONr_scangle_it4.3174.51671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 74 -
Rwork0.373 1387 -
obs--99.52 %

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