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Yorodumi- PDB-4xx6: Crystal structure of a glycosylated endo-beta-1,4-xylanase (glyco... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4xx6 | |||||||||
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| Title | Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Gloeophyllum trabeum | |||||||||
Components | Beta-xylanase | |||||||||
Keywords | HYDROLASE / XYLANASE / FUNGUS / TIM BARREL / ALPHA8/BETA8 FOLD / GLYCOSIDE HYDROLASE FAMILY 10 / GH10 | |||||||||
| Function / homology | Function and homology informationendo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process / metal ion binding Similarity search - Function | |||||||||
| Biological species | Gloeophyllum trabeum (fungus) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Stogios, P.J. / Nocek, B. / Xu, X. / Cui, H. / Lowden, M. / Savchenko, A. | |||||||||
Citation | Journal: To Be PublishedTitle: Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Gloeophyllum trabeum. Authors: Stogios, P.J. / Xu, X. / Cui, H. / Lowden, M. / Savchenko, A. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4xx6.cif.gz | 293.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4xx6.ent.gz | 238.2 KB | Display | PDB format |
| PDBx/mmJSON format | 4xx6.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4xx6_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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| Full document | 4xx6_full_validation.pdf.gz | 2.7 MB | Display | |
| Data in XML | 4xx6_validation.xml.gz | 33.9 KB | Display | |
| Data in CIF | 4xx6_validation.cif.gz | 50.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/4xx6 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/4xx6 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 3cuiS S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
| #1: Protein | Mass: 35700.574 Da / Num. of mol.: 2 / Fragment: UNP residues 27-347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeophyllum trabeum (fungus) / Strain: ATCC 11539 / FP-39264 / Madison 617 / Gene: GLOTRDRAFT_138785 / Plasmid: ANIp7G / Production host: ![]() |
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-Sugars , 7 types, 9 molecules 
| #2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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| #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #5: Polysaccharide | alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #9: Sugar |
-Non-polymers , 7 types, 598 molecules 












| #8: Chemical | | #10: Chemical | #11: Chemical | #12: Chemical | #13: Chemical | ChemComp-GOL / #14: Chemical | ChemComp-CL / | #15: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION |
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Sample preparation
| Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
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| Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Tris, pH 8.5, 0.2 M magnesium chloride, 30% (w/v) PEG 4K, subtlisin protease |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
| Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2012 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
| Reflection | Resolution: 1.95→40 Å / Num. obs: 53797 / % possible obs: 94.5 % / Redundancy: 2.7 % / Rsym value: 0.036 / Net I/σ(I): 20.98 |
| Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.84 / % possible all: 89.5 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 3CUI Resolution: 1.95→30.2 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.61 / Stereochemistry target values: ML
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.95→30.2 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group |
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Gloeophyllum trabeum (fungus)
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