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- PDB-6jxl: 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: 6jxl | |||||||||
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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 / 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, Z. / Wan, Q. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose Authors: Wan, Q. #1: ![]() Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism Authors: Wan, Q. / Qiu, Z. #2: ![]() Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography Authors: Wan, Q. / Jerry, M.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.2 KB | Display | ![]() |
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PDB format | ![]() | 99.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.9 KB | Display | ![]() |
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Full document | ![]() | 732.2 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zf3C ![]() 2dfcS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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: 20728.322 Da / Num. of mol.: 1 / Fragment: UNP residues 35-223 / Mutation: N44D 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 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 280 K / Method: evaporation / pH: 6 / Details: 20%PEG 8000, 0.2M NaI,0.1M MES |
-Data collection
Diffraction | Mean temperature: 280 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: 1.3→44.965 Å / Num. obs: 39057 / % possible obs: 80.04 % / Redundancy: 5.5 % / Biso Wilson estimate: 13.4 Å2 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.3→1.347 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1793 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DFC Resolution: 1.3→32.67 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.77 Å2 / Biso mean: 18.7787 Å2 / Biso min: 7.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→32.67 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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