+Open data
-Basic information
Entry | Database: PDB / ID: 2pg5 | ||||||
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Title | Crystal Structure of Human Microsomal P450 2A6 N297Q | ||||||
Components | Cytochrome P450 2A6 | ||||||
Keywords | OXIDOREDUCTASE / CYP2A6 / P450 2A6 / P450 / Monooxygenases / drug metabolizing enzyme / heme / mutant / indole | ||||||
Function / homology | Function and homology information coumarin catabolic process / coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / arachidonic acid epoxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification ...coumarin catabolic process / coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / arachidonic acid epoxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification / Xenobiotics / 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 / aromatase activity / steroid metabolic process / cytoplasmic microtubule / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Sansen, S. / Hsu, M.H. / Stout, C.D. / Johnson, E.F. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2007 Title: Structural insight into the altered substrate specificity of human cytochrome P450 2A6 mutants. Authors: Sansen, S. / Hsu, M.H. / Stout, C.D. / Johnson, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pg5.cif.gz | 387 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pg5.ent.gz | 316.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pg5 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pg5 | HTTPS FTP |
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-Related structure data
Related structure data | 2pg6C 2pg7C 1z10S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Details | The biological assembly has not been determined but thought to be a monomer |
-Components
#1: Protein | Mass: 54685.664 Da / Num. of mol.: 4 / Mutation: N297Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A6 / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DC5 References: UniProt: P11509, UniProt: Q16696*PLUS, unspecific monooxygenase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG3350, Tris, ammonium sulfate, Anapoe-35, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2006 Details: flat mirror (vertical focussing) ; single crystal Si(111) bent monochromator (horizontal focussing) |
Radiation | Monochromator: Side scattering bent cube-root I-beam crystal; asymmetric cut 4.965 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35 Å / Num. all: 163342 / Num. obs: 163342 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Χ2: 3.194 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.5 / Num. unique all: 15732 / Rsym value: 0.383 / Χ2: 1.183 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: coumarin complex of CYP2A6, PDB entry 1Z10 Resolution: 1.95→35 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 39.806 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.387 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.04 Å / Rfactor Rfree error: 0.011
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Xplor file |
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