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- PDB-2hyk: The crystal structure of an endo-beta-1,3-glucanase from alkaliph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hyk | ||||||
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Title | The crystal structure of an endo-beta-1,3-glucanase from alkaliphilic Nocardiopsis sp.strain F96 | ||||||
![]() | Beta-1,3-glucanase | ||||||
![]() | HYDROLASE / family 16 / beta-jelly roll / bacterial endo-beta-1 / 3-glucanase | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fibriansah, G. / Nakamura, S. / Kumasaka, T. | ||||||
![]() | ![]() Title: The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96. Authors: Fibriansah, G. / Masuda, S. / Koizumi, N. / Nakamura, S. / Kumasaka, T. #1: ![]() Title: Crystallization and preliminary crystallographic analysis of endo-beta-1,3-beta-glucanase from alkaliphilic Nocardiopsis sp. strain F96 Authors: Fibriansah, G. / Masuda, S. / Hirose, R. / Hamada, K. / Tanaka, N. / Nakamura, S. / Kumasaka, 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 | ![]() | 111.2 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.2 KB | Display | ![]() |
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Full document | ![]() | 452.9 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27127.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q2V0H0, glucan endo-1,3-beta-D-glucosidase |
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-Non-polymers , 5 types, 224 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / | ||||
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#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 31.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl pH 8.0, 1.3-1.4M Ammonium sulfate, 1% Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2004 / Details: rhodium-coated mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.4 % / Av σ(I) over netI: 11.1 / Number: 166200 / Rmerge(I) obs: 0.09 / Χ2: 1.78 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 25958 / % possible obs: 99.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.3→50 Å / Num. obs: 47558 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.064 / Χ2: 1.766 / Net I/σ(I): 14.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.35 / Num. unique all: 4574 / Χ2: 1.157 / % possible all: 95.7 |
-Phasing
Phasing | Method: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Phasing dm | FOM : 0.71 / FOM acentric: 0.71 / FOM centric: 0.69 / Reflection: 24080 / Reflection acentric: 23426 / Reflection centric: 654 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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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: 9.249 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→39.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.297→1.331 Å / Total num. of bins used: 20
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