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Yorodumi- PDB-2dsk: Crystal structure of catalytic domain of hyperthermophilic chitin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dsk | ||||||
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Title | Crystal structure of catalytic domain of hyperthermophilic chitinase from Pyrococcus furiosus | ||||||
Components | chitinase | ||||||
Keywords | HYDROLASE / chitinase / catalytic domain / active domain / crystalline chitin / TIM-barrel | ||||||
Function / homology | Function and homology information polysaccharide binding / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Nakamura, T. / Mine, S. / Hagihara, Y. / Ishikawa, K. / Uegaki, K. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2007 Title: Structure of the catalytic domain of the hyperthermophilic chitinase from Pyrococcus furiosus Authors: Nakamura, T. / Mine, S. / Hagihara, Y. / Ishikawa, K. / Uegaki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dsk.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dsk.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/2dsk ftp://data.pdbj.org/pub/pdb/validation_reports/ds/2dsk | 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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-Components
#1: Protein | Mass: 34764.227 Da / Num. of mol.: 2 / Fragment: catalutic domain (AD2) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8U1H5, chitinase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / | #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: 3.22 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, pH 6.5, 1.6M magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 142710 / Num. obs: 142710 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.107 | ||||||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→25.19 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2059927.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.335 Å2 / ksol: 0.395384 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→25.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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