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- PDB-4jlt: Crystal structure of P450 2B4(H226Y) in complex with paroxetine -

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Basic information

Entry
Database: PDB / ID: 4jlt
TitleCrystal structure of P450 2B4(H226Y) in complex with paroxetine
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / P450 / cytochrome P450 2B4 / monooxygenase / ME protein / CYP 2B4
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
Paroxetine / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsShah, M.B. / Pascual, J. / Stout, C.D. / Halpert, J.R.
CitationJournal: J.Pharmacol.Exp.Ther. / Year: 2013
Title: A Structural Snapshot of CYP2B4 in Complex with Paroxetine Provides Insights into Ligand Binding and Clusters of Conformational States.
Authors: Shah, M.B. / Kufareva, I. / Pascual, J. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)57,26513
Polymers54,1691
Non-polymers3,09612
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.760, 90.760, 153.681
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 54169.082 Da / Num. of mol.: 1 / Fragment: Cytochrome P450 2B4 / Mutation: 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

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Non-polymers , 7 types, 231 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-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.: 3 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-8PR / Paroxetine / (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine


Mass: 329.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20FNO3 / Comment: antidepressant, inhibitor*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS INFORMED THAT THE GENBANK SEQUENCE IS THOUGHT TO CONTAIN A SEQUENCING ERROR 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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 2M Ammonium Sulfate, pH 7.5, 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 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 11, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.137→78.6 Å / Num. all: 41220 / Num. obs: 41055 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 8.2
Reflection shellResolution: 2.137→2.25 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.444 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MVR

3mvr


Resolution: 2.14→78.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.243 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2066 5 %RANDOM
Rwork0.187 ---
all0.19 39214 --
obs0.19 38955 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 172.23 Å2 / Biso mean: 40.305 Å2 / Biso min: 15.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.14→78.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 183 219 4056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223927
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9042.0485336
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50622.931174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91515620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4051530
X-RAY DIFFRACTIONr_chiral_restr0.130.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212911
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_it1.1021.52286
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98723711
X-RAY DIFFRACTIONr_scbond_it3.03731641
X-RAY DIFFRACTIONr_scangle_it4.674.51625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 161 -
Rwork0.224 2832 -
all-2993 -
obs-2832 99.04 %

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