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- PDB-1nr6: MICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH DICLOFENAC -

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Basic information

Entry
Database: PDB / ID: 1nr6
TitleMICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH DICLOFENAC
ComponentsCYTOCHROME P450 2C5
KeywordsOXIDOREDUCTASE / MEMBRANE PROTEIN / PROGESTERONE 21-HYDROXYLASE / BENZO(A) / PYRENE HYDROXYLASE / ESTRADIOL 2-HYDROXYLASE / P450 / CYP2C5 / DICLOFENAC COMPLEX
Function / homology
Function and homology information


organic acid metabolic process / unspecific monooxygenase / aromatase activity / 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
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2C5
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWester, M.R. / Johnson, E.F. / Stout, C.D.
CitationJournal: Biochemistry / Year: 2003
Title: Structure of Mammalian Cytochrome P450 2C5 Complexed with Diclofenac at 2.1 A Resolution: Evidence for an Induced Fit Model of Substrate Binding
Authors: WESTER, M.R. / JOHNSON, E.F. / Marques-Soares, C. / Dijols, S. / Dansette, P.M. / Mansuy, D. / STOUT, C.D.
History
DepositionJan 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: 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_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 1.4Aug 16, 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 2C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9895
Polymers53,8841
Non-polymers1,1054
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.94, 130.02, 172.78
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-762-

HOH

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Components

#1: Protein CYTOCHROME P450 2C5 / CYPIIC5 / PROGESTERONE 21-HYDROXYLASE / P450 1 / 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 / 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-DIF / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / DICLOFENAC


Mass: 296.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11Cl2NO2 / Comment: antiinflammatory, medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: AMMONIUM SULFATE, CYMAL5, pH 7.0, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.24 mMprotein1drop
20.24 mMdiclofenac1drop
32.4 mMCYMAL-5 detergent1drop
41.1 Mammonium sulfate1drop
50.05 MHEPES1droppH7.8
60.5 %PEG4001drop
720 mMpotassium phosphate1droppH7.4
8200 mM1dropNaCl
90.4 mMEDTA1drop
100.08 mMdithiothreitol1drop
118 %glycerol1drop
122.2 Mammonium sulfate1reservoir
130.1 MHEPES1reservoirpH7.8
141 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2001
RadiationMonochromator: FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48402 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.565 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 185186
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
SSRLBLU-ICEdata collection
MOSFLMdata reduction
CCP4SCALAdata reduction
CNSrefinement
Blu-Icedata collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N6B
Resolution: 2.1→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 4344 RANDOM
Rwork0.231 --
all0.231 48402 -
obs0.231 48402 -
Displacement parametersBiso mean: 46.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati sigma a0.31 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 72 262 4032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.34
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.349 421 -
Rwork0.323 --
obs-7130 98.5 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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