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Yorodumi- PDB-1gyo: Crystal structure of the di-tetraheme cytochrome c3 from Desulfov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gyo | ||||||
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Title | Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution | ||||||
Components | CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME C3 / DI-TETRAHEME / AB INITIO / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | DESULFOVIBRIO GIGAS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.2 Å | ||||||
Authors | Aragao, D. / Frazao, C. / Sieker, L. / Sheldrick, G.M. / Legall, J. / Carrondo, M.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of Dimeric Cytochrome C3 from Desulfovibrio Gigas at 1.2 A Resolution Authors: Aragao, D. / Frazao, C. / Sieker, L. / Sheldrick, G.M. / Legall, J. / Carrondo, M.A. #1: Journal: J.Biol.Inorg.Chem. / Year: 1999 Title: Ab Initio Structure Solution of a Dimeric Cytochrome C3 from Desulfovibrio Gigas Containing Disulfide Bridges Authors: Frazao, C. / Sieker, L. / Sheldrick, G.M. / Lamzin, V. / Legall, J. / Carrondo, M.A. #2: Journal: FEBS Lett. / Year: 1986 Title: Preliminary X-Ray Studies of the Tetra-Heme Cytochrome C3 and the Octa-Heme Cytochrome C3 from Desulfovibrio Gigas Authors: Sieker, L.C. / Jensen, L.H. / Legall, J. / 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 | 1gyo.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gyo.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/1gyo ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gyo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.5378, 0.8381, 0.0914), Vector: |
-Components
#1: Protein | Mass: 12240.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO GIGAS (bacteria) / References: UniProt: Q9R638 #2: Chemical | ChemComp-HEC / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | pH: 6.5 Details: SALTING OUT FROM A PROTEIN SOLUTION IN TRIS/MALEATE PH=6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1037 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1037 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→26.44 Å / Num. obs: 104411 / % possible obs: 98.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.2→1.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.8 / % possible all: 95.6 |
Reflection shell | *PLUS % possible obs: 95.6 % |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1.2→26.5 Å / Num. parameters: 21173 / Num. restraintsaints: 50776 / Cross valid method: THROUGHOUT / σ(F): 0 StereochEM target val spec case: HEME GROUPS WERE RESTRAINED TO BE SIMILAR BUT WITHOUT TARGET VALUES, DUE TO THEIR INTERNAL SYMMETRY AND FOUR- OR EIGHT-FOLD REDUNDANCY Stereochemistry target values: ENGH & HUBER Details: C-TERMINI RESIDUES ALA107-GLN108- LYS109 ARE MISSING IN EACH MONOMER AS THEY ARE NOT VISIBLE IN ELECTRON DENSITY MAPS. SOLVENT WATER MOLECULES THAT FOLLOW THE INTER-MONOMERS NCS RELATIONSHIP ...Details: C-TERMINI RESIDUES ALA107-GLN108- LYS109 ARE MISSING IN EACH MONOMER AS THEY ARE NOT VISIBLE IN ELECTRON DENSITY MAPS. SOLVENT WATER MOLECULES THAT FOLLOW THE INTER-MONOMERS NCS RELATIONSHIP ARE DIVIDED INTO TWO CHAINS, X FOR THOSE CLOSE TO MONOMER A AND Y FOR THOSE CLOSE TO MONOMER B. OTHER SOLVENT MOLECULES ARE ASSIGNED TO CHAIN Z. THE GLYCEROL MOLECULES IN THE STRUCTURE ARE ARTIFACTS OF THE CRYO- PROTECTANT.
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 19 / Occupancy sum non hydrogen: 2286 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→26.5 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.2 Å / Rfactor obs: 0.124 / Rfactor Rfree: 0.148 / Rfactor Rwork: 0.124 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |