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Yorodumi- PDB-1ofy: three dimensional structure of the reduced form of nine-heme cyto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofy | ||||||
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Title | three dimensional structure of the reduced form of nine-heme cytochrome c at ph 7.5 | ||||||
Components | NINE HEME CYTOCHROME C | ||||||
Keywords | ELECTRON TRANSPORT / MULTIHEME CYTOCHROME C / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO DESULFURICANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bento, I. / Teixeira, V.H. / Baptista, A.M. / Soares, C.M. / Matias, P.M. / Carrondo, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Redox-Bohr and Other Cooperativity Effects in the Nine-Heme Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies Authors: Bento, I. / Teixeira, V.H. / Baptista, A.M. / Soares, C.M. / Matias, P.M. / 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 | 1ofy.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofy.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 1ofy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofy ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofy | HTTPS FTP |
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-Related structure data
Related structure data | 1ofwC 19hcS 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: 32264.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q9RN68 #2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: 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: 3.3 Å3/Da / Density % sol: 62.7 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop / Details: Coelho, A.V., (1996) Protein Sci., 5, 1189. | ||||||||||||||||||||||||
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: ESRF / Beamline: BM14 / Wavelength: 0.8 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 65158 / % possible obs: 97.6 % / Redundancy: 2.72 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.69 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 25 Å / Redundancy: 2.72 % / Num. measured all: 177499 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 98 % / Rmerge(I) obs: 0.371 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 19HC Resolution: 2→25 Å / Num. parameters: 23131 / Num. restraintsaints: 28791 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 9 / Occupancy sum non hydrogen: 5701 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.237 / Rfactor Rwork: 0.185 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |