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Yorodumi- PDB-2y6k: Xylotetraose bound to X-2 engineered mutated CBM4-2 Carbohydrate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y6k | |||||||||
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Title | Xylotetraose bound to X-2 engineered mutated CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase | |||||||||
Components | XYLANASE | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||
Biological species | RHODOTHERMUS MARINUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | |||||||||
Authors | von Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M. | |||||||||
Citation | Journal: Glycobiology / Year: 2012 Title: Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules. Authors: von Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y6k.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y6k.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 2y6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6k ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6k | HTTPS FTP |
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-Related structure data
Related structure data | 2y64C 2y6gC 2y6hC 2y6jSC 2y6lC C: citing same article (ref.) S: Starting model for refinement |
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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: 17905.717 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): T7 EXPRESS References: UniProt: Q6V8M0, UniProt: Q7WTN6*PLUS, endo-1,4-beta-xylanase | ||||||||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source | ||||||||
#3: Chemical | #4: Chemical | ChemComp-CIT / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TRP 68 TO PHE ENGINEERED RESIDUE IN CHAIN A, ASP 69 TO ASN ...ENGINEERED | Sequence details | THIS CONSTRUCT STARTS WITH M (POSITION 1) AND ENDS WITH ONE L | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42.8 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 1.2 M SODIUM CITRATE PH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Sep 25, 2008 / Details: MULTILAYER MIRROR |
Radiation | Monochromator: BENT SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0379 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→30 Å / Num. obs: 32599 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.36→1.4 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.3 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y6J Resolution: 1.36→30 Å / Num. parameters: 14368 / Num. restraintsaints: 18261 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 21 / Occupancy sum hydrogen: 1233 / Occupancy sum non hydrogen: 1530.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→30 Å
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Refine LS restraints |
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