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Yorodumi- PDB-1c6o: CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GREEN ALGAE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c6o | ||||||
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Title | CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GREEN ALGAE SCENEDESMUS OBLIQUUS | ||||||
Components | CYTOCHROME C6 | ||||||
Keywords | ELECTRON TRANSPORT / ELECTRON TRANSPORT PROTEIN / CYTOCHROME-C6 / OXIDIZED STATE / PHOTOSYNTHESIS / DIMERIZATION | ||||||
Function / homology | Function and homology information chloroplast thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Scenedesmus obliquus (plant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schnackenberg, J. / Than, M.E. / Mann, K. / Wiegand, G. / Huber, R. / Reuter, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Amino acid sequence, crystallization and structure determination of reduced and oxidized cytochrome c6 from the green alga Scenedesmus obliquus. Authors: Schnackenberg, J. / Than, M.E. / Mann, K. / Wiegand, G. / Huber, R. / Reuter, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c6o.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c6o.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 1c6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/1c6o ftp://data.pdbj.org/pub/pdb/validation_reports/c6/1c6o | HTTPS FTP |
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-Related structure data
Related structure data | 1c6rSC 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: 9415.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GENE IS NUCLEAR PETJ / Source: (natural) Scenedesmus obliquus (plant) / Cellular location: THYLAKOID LUMEN OF CHLOROPLAST / Organelle: CHLOROPLAST / Strain: D3 / References: UniProt: P57736 #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: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 14441 / % possible obs: 98.7 % / Redundancy: 5 % / Biso Wilson estimate: 39.6 Å2 / Rsym value: 6.6 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 34.4 / % possible all: 92.4 |
Reflection | *PLUS Num. measured all: 75095 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 92.4 % / Rmerge(I) obs: 0.342 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C6R Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2 Details: OCCUPANCY AND B-FACTOR ARE SET TO ZERO FOR ALL ATOMS THAT ARE NOT DEFINED IN THE FINAL 2FO-FC ELECTRON DENSITY.
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Displacement parameters | Biso mean: 32.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Total num. of bins used: 20
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 9.43 % / Rfactor obs: 0.2175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Num. reflection obs: 552 / Rfactor obs: 0.3751 |