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- PDB-6bww: Crystal structure of an acetate and Cymal-5 bound cytochrome P450... -

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Basic information

Entry
Database: PDB / ID: 6bww
TitleCrystal structure of an acetate and Cymal-5 bound cytochrome P450 2B4 F429H mutant
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / Acetate Cymal-5 / P450 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsYang, Y.T. / Waskell, L.
Funding support United States, 1items
OrganizationGrant numberCountry
United States
CitationJournal: J.Inorg.Biochem. / Year: 2018
Title: Structure of cytochrome P450 2B4 with an acetate ligand and an active site hydrogen bond network similar to oxyferrous P450cam.
Authors: Yang, Y. / Bu, W. / Im, S. / Meagher, J. / Stuckey, J. / Waskell, L.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)56,24818
Polymers53,6181
Non-polymers2,63117
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.185, 93.185, 151.092
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: 53617.508 Da / Num. of mol.: 1 / Mutation: F429H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2B4 / Production host: Escherichia coli (E. coli) / References: UniProt: P00178, unspecific monooxygenase

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Non-polymers , 5 types, 315 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.: 2 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 277 K / Method: evaporation
Details: mixing 2 ul of protein and 2 ul of reservoir solution containing 0.2 M magnesium acetate, 0.1 M cacodylate pH 6.5, 10-15% PEG 3350, and to each drop add 0.4 ul of 10% Anapoe-C10E9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97852 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 44827 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.95 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.244 / Net I/σ(I): 15.6 / Num. measured all: 277140
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.146.30.4122130.99199.5
2.14-2.186.30.3522101.027199.5
2.18-2.226.30.30822151.042199.4
2.22-2.266.20.25421931.107199.4
2.26-2.316.30.22522031.148199.6
2.31-2.376.30.19722091.132199.4
2.37-2.426.20.16922041.14199.8
2.42-2.496.30.14622271.139199.6
2.49-2.566.30.12622211.148199.6
2.56-2.656.20.10322401.145199.9
2.65-2.746.20.09622271.18199.7
2.74-2.856.20.08222061.3199.7
2.85-2.986.20.07922501.323199.9
2.98-3.146.20.07322281.564199.9
3.14-3.336.20.06322621.685199.9
3.33-3.596.20.05222541.551100
3.59-3.956.20.04222681.4081100
3.95-4.526.10.03722871.3321100
4.52-5.760.03423111.261100
5.7-1005.60.03523991.259197.9

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.1→46.59 Å / Cor.coef. Fo:Fc: 0.9463 / Cor.coef. Fo:Fc free: 0.9389 / SU R Cruickshank DPI: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.15 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.132
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 4477 9.99 %RANDOM
Rwork0.1852 ---
obs0.1872 44799 99.57 %-
Displacement parametersBiso max: 147.76 Å2 / Biso mean: 40.92 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.6263 Å20 Å20 Å2
2---0.6263 Å20 Å2
3---1.2527 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: final / Resolution: 2.1→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 291 298 4293
Biso mean--63.27 47.64 -
Num. residues----463
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1715SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1131HARMONIC5
X-RAY DIFFRACTIONt_it7846HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion499SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8885SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7846HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg14172HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion15.54
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2418 319 9.87 %
Rwork0.2026 2912 -
all0.2065 3231 -
obs--99.57 %

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