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- PDB-1n6b: Microsomal Cytochrome P450 2C5/3LVdH Complex with a dimethyl deri... -

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Basic information

Entry
Database: PDB / ID: 1n6b
TitleMicrosomal Cytochrome P450 2C5/3LVdH Complex with a dimethyl derivative of sulfaphenazole
ComponentsCytochrome P450 2C5
KeywordsOXIDOREDUCTASE / MEMBRANE PROTEIN / PROGESTERONE 21-HYDROXYLASE / BENZO(A) / PYRENE HYDROXYLASE / ESTRADIOL 2-HYDROXYLASE / P450 / CYP2C5 / DIMETHYLSULFAPHENAZOLE COMPLEX
Function / homology
Function and homology information


organic acid metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
: / 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
Chem-DMZ / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2C5
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWester, M.R. / Johnson, E.F. / Marques-Soares, C. / Dansette, P.M. / Mansuy, D. / Stout, C.D.
Citation
Journal: Biochemistry / Year: 2003
Title: Structure of a Substrate Complex of Mammalian Cytochrome P450 2C5 at 2.3 A Resolution: Evidence for Multiple Substrate Binding Modes
Authors: Wester, M.R. / Johnson, E.F. / Marques-Soares, C. / Dansette, P.M. / Mansuy, D. / Stout, C.D.
#1: Journal: Mol.Cell / Year: 2000
Title: Mammalian Microsomal Cytochrome P450 Monooxygenase: Structural Adaptations for Membrane Binding and Functional Diversity
Authors: Williams, P.A. / Cosme, J. / Sridhar, V. / Johnson, E.F. / McRee, D.E.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Engineering Microsomal Cytochrome P450 2C5 to be a Soluble, Monomeric Enzyme. Mutations that Alter Aggregation, Phospholipid Dependence of Catalysis, and Membrane Binding
Authors: Cosme, J. / Johnson, E.F.
History
DepositionNov 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 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.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_conn.ptnr2_label_seq_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 1.4Feb 14, 2024Group: 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 2C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0205
Polymers53,8841
Non-polymers1,1364
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Cytochrome P450 2C5
hetero molecules

A: Cytochrome P450 2C5
hetero molecules

A: Cytochrome P450 2C5
hetero molecules

A: Cytochrome P450 2C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,08120
Polymers215,5374
Non-polymers4,54416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area15900 Å2
ΔGint-242 kcal/mol
Surface area75480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.330, 134.290, 171.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

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Components

#1: Protein Cytochrome P450 2C5 / CYPIIC5 / P450 1 / Progesterone 21-hydroxylase / P450IIC5


Mass: 53884.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2C5 / Organ: LIVER / Plasmid: PCW / Production host: Escherichia coli (E. coli) / References: UniProt: P00179, unspecific monooxygenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-DMZ / 4-METHYL-N-METHYL-N-(2-PHENYL-2H-PYRAZOL-3-YL)BENZENESULFONAMIDE / DIMETHYLSULFAPHENAZOLE


Mass: 327.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: AMMONIUM SULFATE, CYMAL5, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.24 mMP4501drop
20.24 mMDMZ1drop
32.4 mMCYMAL-5 detergent1drop
41.1 Mammonium sulfate1drop
50.05 MHEPES1droppH7.5
60.5 %PEG4001drop
720 mMpotassium phosphate1droppH7.4
8200 mM1dropNaCl
90.4 mMEDTA1drop
100.08 mMdithiothreitol1drop
118 %glycerol1drop
122.2 Mammonium sulfate1reservoir
130.1 MHEPES1reservoirpH7.5
141 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37253 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.479 / % possible all: 78.5
Reflection
*PLUS
Num. measured all: 153575
Reflection shell
*PLUS
% possible obs: 78.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT6

1dt6


Resolution: 2.3→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1698 -RANDOM
Rwork0.257 ---
obs0.257 37253 96.6 %-
all-37253 --
Displacement parametersBiso mean: 60.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 0 76 118 3891
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.29
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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