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- PDB-2q6n: Structure of Cytochrome P450 2B4 with Bound 1-(4-cholorophenyl)im... -

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Basic information

Entry
Database: PDB / ID: 2q6n
TitleStructure of Cytochrome P450 2B4 with Bound 1-(4-cholorophenyl)imidazole
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / p450 / Monooxygenase / membrane protein / CYP 2B4 / CYP LM2
Function / homology
Function and homology information


response to stimulus / unspecific monooxygenase / aromatase activity / 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
1-(4-CHLOROPHENYL)-1H-IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZhao, Y. / Sun, L. / Muralidhara, B.K. / Kumar, S. / White, M.A. / Stout, C.D. / Halpert, J.R.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
Authors: Zhao, Y. / Sun, L. / Muralidhara, B.K. / Kumar, S. / White, M.A. / Stout, C.D. / Halpert, J.R.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 2B4
B: Cytochrome P450 2B4
C: Cytochrome P450 2B4
D: Cytochrome P450 2B4
E: Cytochrome P450 2B4
F: Cytochrome P450 2B4
G: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,68321
Polymers381,1187
Non-polymers5,56614
Water0
1
A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2403
Polymers54,4451
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2403
Polymers54,4451
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2403
Polymers54,4451
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2403
Polymers54,4451
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2403
Polymers54,4451
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2403
Polymers54,4451
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2403
Polymers54,4451
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.000, 147.310, 238.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsEach chain in the asymmetric unit is a biological unit

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Components

#1: Protein
Cytochrome P450 2B4 / CYPIIB4 / P450-LM2 / Isozyme 2 / P450 types B0 and B1


Mass: 54445.371 Da / Num. of mol.: 7
Mutation: E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, P221S, 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
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-1CI / 1-(4-CHLOROPHENYL)-1H-IMIDAZOLE


Mass: 178.618 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H7ClN2

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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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% MPD, 10-12% PEG 6000, and 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→147.442 Å / Num. obs: 81299 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.2-3.284.10.8310.92444859660.831100
3.28-3.374.10.6291.22380358280.629100
3.37-3.474.10.5171.52316856780.517100
3.47-3.584.10.3941.92266255380.394100
3.58-3.74.10.2862.62180953610.28699.9
3.7-3.824.10.2313.22099351620.23199.9
3.82-3.9740.1973.82021750150.19799.9
3.97-4.1340.1584.71947448250.15899.7
4.13-4.3140.1335.41859546080.13399.5
4.31-4.5340.1146.21756544000.11499.3
4.53-4.7740.1016.91657241800.10199.3
4.77-5.0640.0966.91569939720.09699.2
5.06-5.413.90.0966.91447937340.09699.1
5.41-5.843.90.1016.81356534920.10198.7
5.84-6.43.80.0986.81233932230.09899
6.4-7.163.60.097.11046128720.0998
7.16-8.263.50.0738.3878425440.07396.8
8.26-10.123.70.05910.1814421910.05998.1
10.12-14.313.80.05212660617360.05298.6
14.31-147.443.40.04513.933119740.04594.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SUO

1suo


Resolution: 3.2→30 Å / FOM work R set: 0.732 / σ(F): 277
RfactorNum. reflection% reflection
Rfree0.311 4058 5 %
Rwork0.233 --
obs-80849 98.8 %
Solvent computationBsol: 66.988 Å2
Displacement parametersBiso mean: 111.396 Å2
Baniso -1Baniso -2Baniso -3
1--9.55 Å20 Å20 Å2
2--3.669 Å20 Å2
3---5.881 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26138 0 385 0 26523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.2-3.220.389760.34914961572
3.22-3.240.364980.34114751573
3.24-3.270.376880.35315281616
3.27-3.290.385870.34315111598
3.29-3.310.437720.33914891561
3.31-3.340.354770.33915721649
3.34-3.360.371850.3215001585
3.36-3.390.357730.30815091582
3.39-3.420.379710.3315491620
3.42-3.450.444800.33615351615
3.45-3.480.415780.31615131591
3.48-3.510.35920.29515621654
3.51-3.540.316880.28514871575
3.54-3.570.327790.28115131592
3.57-3.60.368750.28715701645
3.6-3.640.319810.28215341615
3.64-3.670.377950.28815321627
3.67-3.710.344830.27515001583
3.71-3.750.346740.27915421616
3.75-3.790.315880.28615531641
3.79-3.840.348610.2415461607
3.84-3.880.349830.26415331616
3.88-3.930.354910.27915161607
3.93-3.980.321660.25615631629
3.98-4.030.347900.25715101600
4.03-4.090.342710.25915541625
4.09-4.140.315780.2515461624
4.14-4.210.324840.22215371621
4.21-4.270.323890.22915011590
4.27-4.340.301700.20215691639
4.34-4.420.325670.22515551622
4.42-4.50.361910.21415271618
4.5-4.580.357840.22415181602
4.58-4.670.312760.2115521628
4.67-4.780.276890.20515301619
4.78-4.890.319830.21915211604
4.89-5.010.255720.19615521624
5.01-5.140.24780.18915381616
5.14-5.290.333880.21315471635
5.29-5.460.261740.19415471621
5.46-5.660.348910.23415471638
5.66-5.880.346840.2415231607
5.88-6.150.369760.25815831659
6.15-6.470.331810.23915261607
6.47-6.870.357860.23915271613
6.87-7.390.295860.18915481634
7.39-8.120.28770.17915421619
8.12-9.270.187950.1515401635
9.27-11.560.258820.16616021684
11.56-300.267750.25316211696
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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