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Yorodumi- PDB-1j0p: Three dimensional Structure of the Y43L mutant of Tetraheme Cytoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j0p | ||||||
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Title | Three dimensional Structure of the Y43L mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F | ||||||
Components | Cytochrome c3 | ||||||
Keywords | ELECTRON TRANSPORT / tetraheme cytochrome c3 / high resolution X-ray structure / Y43L mutant | ||||||
Function / homology | Function and homology information anaerobic respiration / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.91 Å | ||||||
Authors | Ozawa, K. / Yasukawa, F. / Kumagai, J. / Ohmura, T. / Cusanvich, M.A. / Tomimoto, Y. / Ogata, H. / Higuchi, Y. / Akutsu, H. | ||||||
Citation | Journal: Biophys.J. / Year: 2003 Title: Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F. Authors: Ozawa, K. / Takayama, Y. / Yasukawa, F. / Ohmura, T. / Cusanovich, M.A. / Tomimoto, Y. / Ogata, H. / Higuchi, Y. / Akutsu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j0p.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j0p.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 1j0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j0p ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j0p | HTTPS FTP |
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-Related structure data
Related structure data | 1j0oC 1wr5C 2cdvS 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: 11579.344 Da / Num. of mol.: 1 / Mutation: Y43L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Plasmid: pKFC3K / Production host: Shewanella oneidensis (bacteria) / Strain (production host): TSP-C / References: UniProt: P00132 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-EOH / #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: 2.22 Å3/Da / Density % sol: 44.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: small tubes / pH: 7.4 / Details: ethanol, pH 7.4, SMALL TUBES, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 13, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 0.913→26.343 Å / Num. all: 82305 / Num. obs: 82055 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.044 |
Reflection shell | Resolution: 0.91→0.96 Å / Rmerge(I) obs: 0.221 / % possible all: 88.1 |
Reflection | *PLUS Highest resolution: 0.91 Å |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2CDV Resolution: 0.91→10 Å / Num. parameters: 13084 / Num. restraintsaints: 14462 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.035 Å / Num. disordered residues: 2 / Occupancy sum hydrogen: 1019 / Occupancy sum non hydrogen: 1393.98 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.91→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.136 / Rfactor Rwork: 0.1057 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |