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- PDB-8ihx: X-ray crystal structure of N372D mutant of endo-1,4-beta glucanas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ihx | ||||||
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Title | X-ray crystal structure of N372D mutant of endo-1,4-beta glucanase from Eisenia fetida | ||||||
![]() | Endoglucanase | ||||||
![]() | HYDROLASE / earthworm / cellulase / cold-adapted enzyme | ||||||
Function / homology | ![]() cellulase / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuroki, C. / Hirano, Y. / Nakazawa, M. / Sakamoto, T. / Tamada, T. / Ueda, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A single mutation Asp43Arg was increased 2.5-fold the catalytic activity and maintained the stability of cold-adapted endo-1,4-beta glucanase (Ef-EG2) from Eisenia fetida. Authors: Kuroki, C. / Hirano, Y. / Nakazawa, M. / Sakamoto, T. / Tamada, T. / Ueda, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136 KB | Display | ![]() |
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PDB format | ![]() | 82.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 982.5 KB | Display | ![]() |
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Full document | ![]() | 982.9 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ihwC ![]() 8ihyC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51706.066 Da / Num. of mol.: 1 / Mutation: N372D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 425 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% PEG3350, 0.2 M magnesium chloride, 50 mM sodium acetate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 49763 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.35 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.086 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2407 / CC1/2: 0.873 / Rrim(I) all: 0.491 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→48.76 Å
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Refine LS restraints |
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LS refinement shell |
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