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- PDB-1suo: Structure of mammalian cytochrome P450 2B4 with bound 4-(4-chloro... -

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Basic information

Entry
Database: PDB / ID: 1suo
TitleStructure of mammalian cytochrome P450 2B4 with bound 4-(4-chlorophenyl)imidazole
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / membrane protein / CYP 2B4 / CYP LM2 / Cytochrome p450 / Monooxygenase
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
4-(4-CHLOROPHENYL)IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsScott, E.E. / White, M.A. / He, Y.A. / Johnson, E.F. / Stout, C.D. / Halpert, J.R.
Citation
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.
#1: 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.
#2: Journal: Arch.Biochem.Biophys. / Year: 2001
Title: A Truncation of 2B Subfamily Cytochromes P450 Yields Increased Expression Levels, Increased Solubility, and Decreased Aggregation While Retaining Function
Authors: Scott, E.E. / Spatzenegger, M. / Halpert, J.R.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE AUTHORS INFORMED THAT THE GENBANK SEQUENCE IS THOUGHT TO CONTAIN A SEQUENCING ERROR 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)54,9643
Polymers54,1691
Non-polymers7952
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)233.386, 233.386, 56.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1136-

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
Mutation: E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, P221S, H226Y
Source method: isolated from a genetically manipulated source
Details: CYS 436 BINDS HEME IRON. 4-(4-CHLOROPHENYL)IMIDAZOLE IS BOUND IN THE ACTIVE SITE COORDINATING TO THE HEME IRON AS THE SIXTH LIGAND.
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-CPZ / 4-(4-CHLOROPHENYL)IMIDAZOLE


Mass: 178.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7ClN2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: NACL, PEG 10,000, PHOSPHATE-CITRATE PH 4.0, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0001 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. obs: 638636 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PO5

1po5


Resolution: 1.9→49 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 --RANDOM
Rwork0.215 ---
all0.215 ---
obs-638636 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 55 190 3979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.017
LS refinement shellResolution: 1.9→1.95 Å / % reflection obs: 100 %

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