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- PDB-6k9w: Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k9w | ||||||
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Title | Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose | ||||||
![]() | Endo-1,4-beta-xylanase 2 | ||||||
![]() | HYDROLASE / xylanase II / complex / Co-crystallization / 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.8 KB | Display | ![]() |
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PDB format | ![]() | 102.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jugC ![]() 6jwbC ![]() 6k9oC ![]() 6k9rC ![]() 6kw9C ![]() 6kwcC ![]() 6kwdC ![]() 6kwfC ![]() 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
#1: Protein | Mass: 20727.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / Details: 20% PEG 8000, 0.2M NaI, 0.1M MES |
-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: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→30.125 Å / Num. obs: 81794 / % possible obs: 99.54 % / Redundancy: 6.5 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.0295 / Net I/σ(I): 16.37 |
Reflection shell | Resolution: 1.1→1.139 Å / Rmerge(I) obs: 0.0295 / Num. unique obs: 8002 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DFC Resolution: 1.1→30.125 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.06 Å2 / Biso mean: 12.8218 Å2 / Biso min: 4.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.1→30.125 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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