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- PDB-5uap: Crystal Structure of CYP2B6 (Y226H/K262R) in complex with Bornyl ... -

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Basic information

Entry
Database: PDB / ID: 5uap
TitleCrystal Structure of CYP2B6 (Y226H/K262R) in complex with Bornyl Bromide
ComponentsCytochrome P450 2B6
KeywordsOXIDOREDUCTASE / Cytochrome P450
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 / ketone metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / anandamide 8,9 epoxidase activity / anandamide 11,12 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 / ketone metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / estrogen 2-hydroxylase activity / Xenobiotics / Phase I - Functionalization of compounds / 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 / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / 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
Chem-82S / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsShah, M.B. / Halpert, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES0003619 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Halogen-pi Interactions in the Cytochrome P450 Active Site: Structural Insights into Human CYP2B6 Substrate Selectivity.
Authors: Shah, M.B. / Liu, J. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 2B6
B: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,92712
Polymers109,2922
Non-polymers4,63510
Water11,476637
1
A: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9636
Polymers54,6461
Non-polymers2,3175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9636
Polymers54,6461
Non-polymers2,3175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.070, 77.070, 202.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 29 - 490 / Label seq-ID: 10 - 471

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cytochrome P450 2B6 / 1 / 4-cineole 2-exo-monooxygenase / CYPIIB6 / Cytochrome P450 IIB1


Mass: 54646.004 Da / Num. of mol.: 2 / Fragment: UNP residues 30-491 / Mutation: Y226H, K262R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2B6 / Plasmid: pKdH / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P20813, 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
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: 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.: 6 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-82S / (1R,2R,4R)-2-bromo-1,7,7-trimethylbicyclo[2.2.1]heptane


Mass: 217.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Bis-Tris pH 6.5 16% w/v PEG10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2013
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.03→55.7 Å / Num. obs: 86395 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 10.8
Reflection shellResolution: 2.03→2.14 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.8 / Num. unique all: 12631 / % possible all: 99.38

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I91

4i91


Resolution: 2.03→50.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.504 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4320 5 %RANDOM
Rwork0.163 ---
obs0.165 82008 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.09 Å20 Å2
2--0.09 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.03→50.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7452 0 224 637 8313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197925
X-RAY DIFFRACTIONr_bond_other_d0.0040.027593
X-RAY DIFFRACTIONr_angle_refined_deg2.0112.00410763
X-RAY DIFFRACTIONr_angle_other_deg1.2353.00317479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.622.893363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0061558
X-RAY DIFFRACTIONr_chiral_restr0.230.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218725
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021909
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 30228 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.03→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 336 -
Rwork0.247 6044 -
obs--99.38 %

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