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- PDB-2d0s: Crystal structure of the Cytochrome C552 from moderate thermophil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2d0s | ||||||
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Title | Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus | ||||||
![]() | cytochrome c | ||||||
![]() | ELECTRON TRANSPORT / HEME PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nakamura, S. / Ichiki, S.I. / Takashima, H. / Uchiyama, S. / Hasegawa, J. / Kobayashi, Y. / Sambongi, Y. / Ohkubo, T. | ||||||
![]() | ![]() Title: Structure of Cytochrome c552 from a Moderate Thermophilic Bacterium, Hydrogenophilus thermoluteolus: Comparative Study on the Thermostability of Cytochrome c Authors: Nakamura, S. / Ichiki, S.I. / Takashima, H. / Uchiyama, S. / Hasegawa, J. / Kobayashi, Y. / Sambongi, Y. / Ohkubo, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.6 KB | Display | ![]() |
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PDB format | ![]() | 19.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.3 KB | Display | ![]() |
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Full document | ![]() | 792.2 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
#1: Protein | Mass: 8566.167 Da / Num. of mol.: 1 / Fragment: residues 1-79 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pKK223-3, pEC86 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (w/v) polyethylene glycol 4000, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2004 / Details: confocal mirror optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 4086 / Num. obs: 4086 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.65 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 4.67 / Num. unique all: 314 / % possible all: 75.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.466 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→9.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.25 Å / Total num. of bins used: 20
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