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Yorodumi- PDB-6k9r: Crystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k9r | |||||||||
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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 / complex / 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: 1.3 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. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2014 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. / Langan, P. / Graham, D. / Kovalevsky, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k9r.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k9r.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 6k9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/6k9r ftp://data.pdbj.org/pub/pdb/validation_reports/k9/6k9r | HTTPS FTP |
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-Related structure data
Related structure data | 6jugC 6jwbC 6k9oC 6k9wC 6kw9C 6kwcC 6kwdC 6kwfC 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
#1: Protein | Mass: 20741.363 Da / Num. of mol.: 1 / Mutation: N44E, E177Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoderma reesei RUT C-30 (fungus) / Strain: Rut C-30 / Gene: xyn2 / Production host: Escherichia coli (E. coli) / References: UniProt: P36217, endo-1,4-beta-xylanase | ||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6 / 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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å |
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→39.974 Å / Num. obs: 42619 / % possible obs: 85.43 % / Redundancy: 6.8 % / Biso Wilson estimate: 5.73 Å2 / Rsym value: 0.0319 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.3→1.346 Å / Num. unique obs: 4849 / Rsym value: 0.0319 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DFC Resolution: 1.3→39.974 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.1 Å2 / Biso mean: 8.8581 Å2 / Biso min: 1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→39.974 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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