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- PDB-6kwf: Crystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kwf | ||||||
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Title | Crystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed with Xylotriose | ||||||
![]() | Endo-1,4-beta-xylanase 2 | ||||||
![]() | HYDROLASE / Xylanase II / Xylotriose | ||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, C. / Wan, Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography. Authors: Li, Z. / Zhang, X. / Li, C. / Kovalevsky, A. / Wan, Q. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.6 KB | Display | ![]() |
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PDB format | ![]() | 72.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jugC ![]() 6jwbC ![]() 6k9oC ![]() 6k9rC ![]() 6k9wC ![]() 6kw9C ![]() 6kwcC ![]() 6kwdC ![]() 6kwgC ![]() 2dfcS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20815.400 Da / Num. of mol.: 1 / Mutation: N44D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/XYP.gif)
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose |
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#3: Sugar | ChemComp-XYP / |
-Non-polymers , 3 types, 277 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-IOD / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.62 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 4.5 / Details: PEG 8000, NaI, NaAc-HAc |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→19.84 Å / Num. obs: 52630 / % possible obs: 98.3 % / Redundancy: 1.6 % / Biso Wilson estimate: 11.68 Å2 / Rmerge(I) obs: 0.91 / Net I/σ(I): 8.24 |
Reflection shell | Resolution: 1.22→1.264 Å / Rmerge(I) obs: 0.91 / Num. unique obs: 5303 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DFC Resolution: 1.22→19.839 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.71 / Phase error: 15.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.52 Å2 / Biso mean: 15.7247 Å2 / Biso min: 4.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.22→19.839 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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