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- PDB-3ibd: Crystal structure of a cytochrome P450 2B6 genetic variant in com... -

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Basic information

Entry
Database: PDB / ID: 3ibd
TitleCrystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole
ComponentsCytochrome P450 2B6
KeywordsOxidoreductase/Oxidoreductase Inhibitor / P450 / cytochrome P450 2B6 / monooxygenase / oxidoreductase / membrane protein / CYP 2B6 / Endoplasmic reticulum / Heme / Iron / Membrane / Metal-binding / Microsome / Phosphoprotein / Oxidoreductase-Oxidoreductase Inhibitor complex
Function / homology
Function and homology information


testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / cellular ketone metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / estrogen 2-hydroxylase activity / anandamide 8,9 epoxidase activity ...testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / cellular ketone metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / estrogen 2-hydroxylase activity / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / Xenobiotics / 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 / Phase I - Functionalization of compounds / steroid metabolic process / xenobiotic catabolic process / monooxygenase activity / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / heme binding / cytoplasm
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
4-(4-CHLOROPHENYL)IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / THIOCYANATE ION / Cytochrome P450 2B6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGay, S.C. / Sun, L. / Talakad, J.C. / Shah, M.B. / Stout, D.C. / Halpert, J.R.
CitationJournal: Mol.Pharmacol. / Year: 2010
Title: Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.
Authors: Gay, S.C. / Shah, M.B. / Talakad, J.C. / Maekawa, K. / Roberts, A.G. / Wilderman, P.R. / Sun, L. / Yang, J.Y. / Huelga, S.C. / Hong, W.X. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionJul 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Non-polymer description
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 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6639
Polymers54,6461
Non-polymers2,0178
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.573, 55.740, 99.090
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 2B6 / CYPIIB6 / P450 IIB1


Mass: 54646.004 Da / Num. of mol.: 1 / Mutation: Y226H, K262R
Source method: isolated from a genetically manipulated source
Details: Deleted residues 3-21, E2A, R22K, H23K, P24T, N25S, T26S, H27K, D28G, R29K, Y226H, K262R, 4x Cterm His tag
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2B6 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P20813, unspecific monooxygenase

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Non-polymers , 5 types, 184 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-CPZ / 4-(4-CHLOROPHENYL)IMIDAZOLE


Mass: 178.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7ClN2
#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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / pH: 5.5
Details: 0.1 M sodium acetate (pH 5.5), 0.2 M potassium thiocyanate, 10% (w/v) PEG 1000, 10% (w/v) PEG 8000, 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: Jun 19, 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: 6.9 % / Av σ(I) over netI: 4.6 / Number: 223616 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / D res high: 1.998 Å / D res low: 98.451 Å / Num. obs: 32536 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.3449.3599.810.0660.0667.1
4.486.3410010.080.087.5
3.664.4810010.0870.0877.5
3.173.6610010.1070.1077.6
2.833.1710010.1260.1267.6
2.592.8310010.1570.1577.6
2.42.5910010.2090.2097.6
2.242.410010.2930.2937.4
2.112.2410010.4280.4286.1
22.1188.110.4870.4874.1
ReflectionResolution: 1.998→98.451 Å / Num. obs: 32536 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.487 / % possible all: 88.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.23 Å
Translation2.5 Å49.23 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: ENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED

2q6n

1suo

2bdm

3g5n


Resolution: 2→98.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.02 / SU B: 4.01 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1640 5 %RANDOM
Rwork0.178 ---
obs0.181 32494 98.1 %-
all-32545 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-0.26 Å2
2---0.69 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2→98.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 89 176 3964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223925
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7672.0075327
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82522.793179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35815633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7421529
X-RAY DIFFRACTIONr_chiral_restr0.1220.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023007
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21928
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22697
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0611.52346
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92523784
X-RAY DIFFRACTIONr_scbond_it3.0331580
X-RAY DIFFRACTIONr_scangle_it4.8134.51538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 101 -
Rwork0.207 1955 -
obs--84.5 %

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