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- PDB-5dzf: Crystal Structure of the catalytic nucleophile mutant of VvEG16 i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dzf | |||||||||
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Title | Crystal Structure of the catalytic nucleophile mutant of VvEG16 in complex with a mixed-linkage glucan octasaccharide | |||||||||
![]() | endo-glucanase | |||||||||
![]() | HYDROLASE / cell wall / dietary fiber / mixed-linkage glucan / xyloglucan / beta-glucan / glycoside hydrolase / endo-glucanase / grapes / plants / protein structure / GH16 / beta-jelly roll / phylogeny | |||||||||
Function / homology | ![]() licheninase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | McGregor, N.G.S. / Tung, C.C. / Van Petegem, F. / Brumer, H. | |||||||||
![]() | ![]() Title: Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases. Authors: McGregor, N. / Yin, V. / Tung, C.C. / Van Petegem, F. / Brumer, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.9 KB | Display | ![]() |
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PDB format | ![]() | 150 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 931.4 KB | Display | ![]() |
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Full document | ![]() | 936.8 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dzeC ![]() 5dzgC ![]() 5sv8C ![]() 1umzS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23296.938 Da / Num. of mol.: 2 / Fragment: endo-glucanase / Mutation: E88A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/BGC.gif)
#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose |
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#3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose |
#5: Sugar | ChemComp-BGC / |
-Non-polymers , 2 types, 450 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5 mM DTT, 5 mM G3GGG3GGG, 0.5 mM GG3GGG3GGG, 1 mM EDTA, 0.1 M HEPES, 1.6 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2014 Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium silicate flat mirror with Pt, Uncoated, and Pd strips | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→42.974 Å / Num. obs: 60997 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 23.527 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.205 / Rrim(I) all: 0.214 / Χ2: 0.995 / Net I/σ(I): 10.85 / Num. measured all: 738087 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UMZ Resolution: 1.65→42.974 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.41 / Stereochemistry target values: ML
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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 max: 56.83 Å2 / Biso mean: 22.0494 Å2 / Biso min: 7.29 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→42.974 Å
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