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- PDB-5dzg: 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: 5dzg | |||||||||
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Title | Crystal Structure of the catalytic nucleophile mutant of VvEG16 in complex with a xyloglucan tetradecasaccharide | |||||||||
![]() | VvEG16, 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. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dzeC ![]() 5dzfC ![]() 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
#1: Protein | Mass: 23394.051 Da / Num. of mol.: 2 / Fragment: endo-glucanase / Mutation: E88A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.1 % Description: clear, colourless, tetragonal bipyramidal crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10 mg/mL Glc8 XyGOs, 1 mM EDTA, 100 mM pH 6 MES, 20% PEG 6000 PH range: 5.5-6.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2014 / Details: Rh coated flat mirror |
Radiation | Monochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→39.41 Å / Num. obs: 40942 / % possible obs: 98.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.317 / % possible all: 78.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UMZ Resolution: 1.79→39.41 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.41 / 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 mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→39.41 Å
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Refine LS restraints |
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LS refinement shell |
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