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Yorodumi- PDB-1wiy: Crystal Structure Analysis of a 6-coordinated Cytochorome P450 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wiy | ||||||
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Title | Crystal Structure Analysis of a 6-coordinated Cytochorome P450 from Thermus thermophilus HB8 | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / P450 / Cytochrome / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kousumi, Y. / Nakagawa, N. / Kaneko, M. / Yamamoto, H. / Masui, R. / Kuramitsu, S. / Ueyama, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure Analysis of Cytochrome P450 from Thermus thermophilus HB8 Authors: Kousumi, Y. / Nakagawa, N. / Kaneko, M. / Yamamoto, H. / Masui, R. / Kuramitsu, S. / Ueyama, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wiy.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wiy.ent.gz | 125.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/1wiy ftp://data.pdbj.org/pub/pdb/validation_reports/wi/1wiy | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44293.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W59 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | A sequence database reference for this protein does not currently exist. | |
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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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, PEG 4000, glycerol, sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 22, 2002 |
Radiation | Monochromator: fix-exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 67512 / % possible obs: 97.3 % / Observed criterion σ(I): 10 / Biso Wilson estimate: 17.1 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 572057.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.2301 Å2 / ksol: 0.393306 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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