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Yorodumi- PDB-1gu2: Crystal structure of oxidized cytochrome c'' from Methylophilus m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gu2 | ||||||
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Title | Crystal structure of oxidized cytochrome c'' from Methylophilus methylotrophus | ||||||
Components | CYTOCHROME C'' | ||||||
Keywords | OXIDOREDUCTASE(CYTOCHROME) / OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | METHYLOPHILUS METHYLOTROPHUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.19 Å | ||||||
Authors | Enguita, F.J. / Pohl, E. / Rodrigues, A. / Santos, H. / Carrondo, M.A. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2006 Title: Structural Evidence for a Proton Transfer Pathway Coupled with Haem Reduction of Cytochrome C" from Methylophilus Methylotrophus. Authors: Enguita, F.J. / Pohl, E. / Turner, D.L. / Santos, H. / Carrondo, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gu2.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gu2.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 1gu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1gu2 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gu2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13699.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria) Strain: W3A1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9RQB9 #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: 2.69 Å3/Da / Density % sol: 0.43 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8492 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8492 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→25 Å / Num. obs: 109062 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.19→1.26 Å / Redundancy: 2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.95 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.19→50 Å / Num. parameters: 21379 / Num. restraintsaints: 25807 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1887 / Occupancy sum non hydrogen: 2354 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Num. reflection obs: 109062 / % reflection Rfree: 5 % / Rfactor Rfree: 0.167 / Rfactor Rwork: 0.1304 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.19 Å / Lowest resolution: 1.26 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.2021 |