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- PDB-1ofy: three dimensional structure of the reduced form of nine-heme cyto... -
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Open data
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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 | ||||||
![]() | NINE HEME CYTOCHROME C | ||||||
![]() | ELECTRON TRANSPORT / MULTIHEME CYTOCHROME C / ELECTRON TRANSFER | ||||||
Function / homology | ![]() periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bento, I. / Teixeira, V.H. / Baptista, A.M. / Soares, C.M. / Matias, P.M. / Carrondo, M.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.3 KB | Display | ![]() |
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PDB format | ![]() | 128 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ofwC ![]() 19hcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() #2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |