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- PDB-4mgj: Crystal structure of cytochrome P450 2B4 F429H in complex with 4-CPI -

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Basic information

Entry
Database: PDB / ID: 4mgj
TitleCrystal structure of cytochrome P450 2B4 F429H in complex with 4-CPI
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / P450 fold / closed conformation / 4-CPI binding
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
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: 2.41 Å
AuthorsYang, Y. / Zhang, H. / Usharani, D. / Bu, W. / Im, S. / Tarasev, M. / Rwere, F. / Meagher, J. / Sun, C. / Stuckey, J. ...Yang, Y. / Zhang, H. / Usharani, D. / Bu, W. / Im, S. / Tarasev, M. / Rwere, F. / Meagher, J. / Sun, C. / Stuckey, J. / Shaik, S. / Waskell, L.
CitationJournal: Biochemistry / Year: 2014
Title: Structural and Functional Characterization of a Cytochrome P450 2B4 F429H Mutant with an Axial Thiolate-Histidine Hydrogen Bond.
Authors: Yang, Y. / Zhang, H. / Usharani, D. / Bu, W. / Im, S. / Tarasev, M. / Rwere, F. / Pearl, N.M. / Meagher, J. / Sun, C. / Stuckey, J. / Shaik, S. / Waskell, L.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)54,9653
Polymers54,1701
Non-polymers7952
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.490, 91.490, 150.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 54170.090 Da / Num. of mol.: 1 / Mutation: F429H, H226Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2B4 / Plasmid: PLW01 / Production host: Escherichia coli (E. coli) / 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.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEGMENT INDICATED AS EXPRESSION TAG HAS BEEN INTRODUCED TO IMPROVE THE SOLUBILITY OF THE PROTEIN CHAIN

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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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, 10-10% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 28505 / Num. obs: 27822 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 65.66 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→38.31 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.9182 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 2860 10.07 %RANDOM
Rwork0.2188 ---
obs0.2217 25612 98.72 %-
Displacement parametersBiso mean: 75.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.2927 Å20 Å20 Å2
2---1.2927 Å20 Å2
3---2.5853 Å2
Refine analyzeLuzzati coordinate error obs: 0.485 Å
Refinement stepCycle: LAST / Resolution: 2.41→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 55 106 3795
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017462HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9713487HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2018SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1094HARMONIC5
X-RAY DIFFRACTIONt_it7462HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion2.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion475SEMIHARMONIC5
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_contact7887SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.5 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3065 297 10.17 %
Rwork0.2643 2622 -
all0.2686 2919 -
obs--98.72 %
Refinement TLS params.Method: refined / Origin x: 40.5353 Å / Origin y: -5.7275 Å / Origin z: 6.5375 Å
111213212223313233
T0.0715 Å2-0.2538 Å20.0731 Å2-0.0136 Å2-0.1194 Å2---0.0461 Å2
L0.7921 °20.2188 °2-0.339 °2-0.8135 °2-0.414 °2--0.0039 °2
S0.0393 Å °-0.0838 Å °0.058 Å °-0.0623 Å °-0.1238 Å °0.104 Å °-0.0148 Å °0.0847 Å °0.0845 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|28 - A|491 A|501 - A|502 }A28 - 491
2X-RAY DIFFRACTION1{ A|28 - A|491 A|501 - A|502 }A501 - 502

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