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Yorodumi- PDB-6kwf: Crystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed... -
+Open data
-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 | ||||||
Components | Endo-1,4-beta-xylanase 2Xylanase | ||||||
Keywords | HYDROLASE / Xylanase II / Xylotriose | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Trichoderma reesei RUT C-30 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Li, C. / Wan, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Protein J. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kwf.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kwf.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/6kwf ftp://data.pdbj.org/pub/pdb/validation_reports/kw/6kwf | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Trichoderma reesei RUT C-30 (fungus) / Gene: xyn2, M419DRAFT_124931 / Production host: Escherichia coli (E. coli) / References: UniProt: P36217, endo-1,4-beta-xylanase |
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-Sugars , 2 types, 2 molecules
#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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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