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- PDB-6kwg: 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: 6kwg | ||||||
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Title | Crystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed with Xylotriose | ||||||
![]() | Endo-1,4-beta-xylanase 2![]() | ||||||
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Function / homology | ![]() ![]() ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.6 KB | Display | ![]() |
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PDB format | ![]() | 67.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jugC ![]() 6jwbC ![]() 6k9oC ![]() 6k9rC ![]() 6k9wC ![]() 6kw9C ![]() 6kwcC ![]() 6kwdC ![]() 6kwfC ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 20741.363 Da / Num. of mol.: 1 / Mutation: N44E/E177Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose | ||||
#3: Chemical | ChemComp-IOD / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.25 % |
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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![]() |
Reflection | Resolution: 1.694→19.503 Å / Num. obs: 19846 / % possible obs: 91 % / Redundancy: 2.14 % / Biso Wilson estimate: 24.02 Å2 / Rmerge(I) obs: 0.224 / Net I/σ(I): 7.27 |
Reflection shell | Resolution: 1.694→1.755 Å / Rmerge(I) obs: 0.224 / Num. unique obs: 2021 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2DFC Resolution: 1.694→19.503 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.22 Å2 / Biso mean: 33.7989 Å2 / Biso min: 19.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.694→19.503 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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