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Yorodumi- PDB-2nza: Structure and Function Studies of Cytochrome P450 158A1 from Stre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nza | ||||||
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Title | Structure and Function Studies of Cytochrome P450 158A1 from Streptomyces coelicolor A3(2) | ||||||
Components | Cytochrome P450 CYP158A1 | ||||||
Keywords | OXIDOREDUCTASE / streptomyces / Cytochrome P450 oxidoreductase / CYP158A1 / flaviolin / C-C coupling activity | ||||||
Function / homology | Function and homology information biflaviolin synthase / pigment metabolic process / 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 | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Zhao, B. / Waterman, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Different binding modes of two flaviolin substrate molecules in cytochrome P450 158A1 (CYP158A1) compared to CYP158A2. Authors: Zhao, B. / Lamb, D.C. / Lei, L. / Kelly, S.L. / Yuan, H. / Hachey, D.L. / Waterman, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nza.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nza.ent.gz | 131 KB | Display | PDB format |
PDBx/mmJSON format | 2nza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/2nza ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nza | HTTPS FTP |
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-Related structure data
Related structure data | 2dkkSC 2nz5C C: citing same article (ref.) 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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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 45589.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SC8F11.24c / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KZF5 #2: Chemical | #3: 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: 2.93 Å3/Da / Density % sol: 58.04 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2006 |
Radiation | Monochromator: Si 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 23648 / % possible obs: 88.4 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.103 / Rsym value: 0.1 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.9→3.02 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1958 / Rsym value: 0.19 / % possible all: 73.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DKK Resolution: 2.9→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 14.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.03 Å / Rfactor Rfree error: 0.041
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