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Open data
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Basic information
Entry | Database: PDB / ID: 6k9o | ||||||
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Title | Crystal Structure Analysis of Protein | ||||||
![]() | 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, 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. #1: ![]() Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism Authors: Wan, Q. / Zhang, Q. / Hamilton-Brehm, S. / Weiss, K. / Mustyakimov, M. / Coates, L. / Graham, D. / Kovalevsky, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.6 KB | Display | ![]() |
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PDB format | ![]() | 99.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 838.9 KB | Display | ![]() |
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Full document | ![]() | 840.3 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jugC ![]() 6jwbC ![]() 6k9rC ![]() 6k9wC ![]() 6kw9C ![]() 6kwcC ![]() 6kwdC ![]() 6kwfC ![]() 6kwgC ![]() 2dfcS ![]() 4khi 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: 20728.322 Da / Num. of mol.: 1 / Mutation: N44D Source method: isolated from a genetically manipulated source Details: Endo-beta-1,4-xylanase II Complexed with Xylotriose Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.69 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6 / Details: PEG 8000, NaI,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: 1.06→28.231 Å / Num. obs: 90198 / % possible obs: 99.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 8.96 Å2 / Rsym value: 0.024 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 1.06→1.098 Å / Num. unique obs: 8882 / Rsym value: 0.024 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DFC Resolution: 1.06→28.231 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 9.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 210.25 Å2 / Biso mean: 13.4436 Å2 / Biso min: 5.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.06→28.231 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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