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Yorodumi- PDB-3tkt: Crystal structure of CYP108D1 from Novosphingobium aromaticivoran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tkt | ||||||
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Title | Crystal structure of CYP108D1 from Novosphingobium aromaticivorans DSM12444 | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 fold / aromatic hydrocarbon binding of P450 enzyme | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Novosphingobium aromaticivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yang, W. / Bell, S.G. / Wang, H. / Zhou, W. / Bartlam, M. / Wong, L.-L. / Rao, Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme Authors: Bell, S.G. / Yang, W. / Yorke, J.A. / Zhou, W. / Wang, H. / Harmer, J. / Copley, R. / Zhang, A. / Zhou, R. / Bartlam, M. / Rao, Z. / Wong, L.-L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tkt.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tkt.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/3tkt ftp://data.pdbj.org/pub/pdb/validation_reports/tk/3tkt | HTTPS FTP |
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-Related structure data
Related structure data | 1cptS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49348.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Strain: DSM 12444 / Gene: Saro_3162 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2G3H6 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.2M lithium sulfate, 0.1M Tris, 27% PEG 4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 3, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 26342 / Num. obs: 26332 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2582 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: 1CPT Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.226 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 27.721 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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