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Yorodumi- PDB-2d09: A Role for Active Site Water Molecules and Hydroxyl Groups of Sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d09 | ||||||
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Title | A Role for Active Site Water Molecules and Hydroxyl Groups of Substrate for Oxygen Activation in Cytochrome P450 158A2 | ||||||
Components | putative cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / streptomyces / Cytochrome P450 oxidoreductase / CYP158A2 / proton transfer / dioxygen activation | ||||||
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 / structure refinement with starting model / Resolution: 1.8 Å | ||||||
Authors | Zhao, B. / Waterman, M.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Role of active site water molecules and substrate hydroxyl groups in oxygen activation by cytochrome P450 158A2: a new mechanism of proton transfer Authors: Zhao, B. / Guengerich, F.P. / Voehler, M. / Waterman, M.R. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Binding of two flaviolin substrate molecules, oxidative coupling, and crystal structure of Streptomyces coelicolor A3(2) cytochrome P450 158A2 Authors: Zhao, B. / Guengerich, F.P. / Bellamine, A. / Lamb, D.C. / Izumikawa, M. / Lei, L. / Podust, L.M. / Sundaramoorthy, M. / Kalaitzis, J.A. / Reddy, L.M. / Kelly, S.L. / Moore, B.S. / Stec, D. ...Authors: Zhao, B. / Guengerich, F.P. / Bellamine, A. / Lamb, D.C. / Izumikawa, M. / Lei, L. / Podust, L.M. / Sundaramoorthy, M. / Kalaitzis, J.A. / Reddy, L.M. / Kelly, S.L. / Moore, B.S. / Stec, D. / Voehler, M. / Falck, J.R. / Shimada, T. / 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 | 2d09.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d09.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d09_validation.pdf.gz | 831 KB | Display | wwPDB validaton report |
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Full document | 2d09_full_validation.pdf.gz | 848 KB | Display | |
Data in XML | 2d09_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 2d09_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/2d09 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/2d09 | HTTPS FTP |
-Related structure data
Related structure data | 2d0eC 1t93S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44621.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: Q9FCA6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-OXY / | #5: 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: 2.449 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, flaviolin, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.95 Å |
Detector | Type: BRUKER PROTEUM 225 / Detector: CCD / Date: Jun 23, 2005 |
Radiation | Monochromator: Si 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.4 Å / Num. all: 37024 / Num. obs: 35918 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.085 / Rsym value: 0.104 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.336 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: structure refinement with starting model Starting model: PDB ENTRY 1T93 Resolution: 1.8→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 49.895 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.811 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.012
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Xplor file |
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