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- PDB-3qhm: Crystal analysis of the complex structure, E342A-cellotetraose, o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qhm | |||||||||
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Title | Crystal analysis of the complex structure, E342A-cellotetraose, of endocellulase from pyrococcus horikoshii | |||||||||
![]() | 458aa long hypothetical endo-1,4-beta-glucanase | |||||||||
![]() | HYDROLASE / cellulase / endoglucanase / catalytic domain | |||||||||
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: Functional analysis of hyperthermophilic endocellulase from Pyrococcus horikoshii by crystallographic snapshots Authors: Kim, H.-W. / Ishikawa, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary X-ray analysis of endoglucanase from Pyrococcus horikoshii Authors: Kim, H.-W. / Mino, K. / Ishikawa, K. #2: ![]() Title: Structure of hyperthermophilic endocellulase from Pyrococcus horikoshii 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 | ![]() | 244.7 KB | Display | ![]() |
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PDB format | ![]() | 197.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 50.2 KB | Display | |
Data in CIF | ![]() | 69 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3axxC ![]() 3qhnC ![]() 3qhoC ![]() 2zumS C: citing same article ( S: Starting model for refinement |
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Similar 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: 51924.844 Da / Num. of mol.: 3 / Mutation: E342A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | #3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.57 % |
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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: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 73075 / % possible obs: 88.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.328 / % possible all: 77.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZUM Resolution: 2.01→35.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 537235.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.18 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→35.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.14 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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