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- PDB-4dm2: Contribution of disulfide bond toward thermostability in hyperthe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dm2 | ||||||
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Title | Contribution of disulfide bond toward thermostability in hyperthermostable endocellulase | ||||||
![]() | 458aa long hypothetical endo-1,4-beta-glucanase | ||||||
![]() | HYDROLASE / TIM barrel / Glycosyl hydrolase / membrane-bound | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, H.-W. / Ishikawa, K. | ||||||
![]() | ![]() Title: Contribution of disulfide bond toward thermostability in hyperthermostable endocellulase Authors: Kim, H.-W. / Ishikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.1 KB | Display | ![]() |
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PDB format | ![]() | 196.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.6 KB | Display | ![]() |
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Full document | ![]() | 475.2 KB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 63.2 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43296.648 Da / Num. of mol.: 3 / Fragment: UNP residues 34-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.5M ammonium phosphate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 89041 / % possible obs: 99.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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 max: 74.94 Å2 / Biso mean: 14.4759 Å2 / Biso min: 2.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→34.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.948→1.998 Å / Total num. of bins used: 20
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