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Yorodumi- PDB-4ejh: Human Cytochrome P450 2A13 in complex with 4-(methylnitrosamino)-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ejh | ||||||
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Title | Human Cytochrome P450 2A13 in complex with 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) | ||||||
Components | Cytochrome P450 2A13 | ||||||
Keywords | OXIDOREDUCTASE / CYP2A13 / cytochrome P450 2A13 / P450 2A13 / heme protein / monooxygenase / drug metabolism / xenobiotic metabolism / endoplasmic reticulum / membrane | ||||||
Function / homology | Function and homology information coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / 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 ...coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / 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 / monooxygenase activity / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | DeVore, N.M. / Scott, E.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes. Authors: DeVore, N.M. / Scott, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ejh.cif.gz | 739.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ejh.ent.gz | 615.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ejh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ejh_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 4ejh_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 4ejh_validation.xml.gz | 134.4 KB | Display | |
Data in CIF | 4ejh_validation.cif.gz | 177.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/4ejh ftp://data.pdbj.org/pub/pdb/validation_reports/ej/4ejh | HTTPS FTP |
-Related structure data
Related structure data | 4ejgSC 4ejiC 4ejjC 1z10S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 54804.758 Da / Num. of mol.: 8 / Fragment: unp residues 31-494 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A13 / Plasmid: pKK2A13dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: Q16696, unspecific monooxygenase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-0QA / #4: Chemical | #5: 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: 2.87 Å3/Da / Density % sol: 57.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 3350, 0.175 M Tris, and 0.2 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 26, 2010 / Details: RH COAT FLAT MIRROR, TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→83.58 Å / Num. all: 787673 / Num. obs: 198013 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.103 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.4 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CYP2A6 WITH COUMARIN (PDB 1Z10) AND CYP2A13 WITH NICOTINE MOLECULE G (PDB 4EJG) Resolution: 2.35→69.77 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.644 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→69.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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