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Yorodumi- PDB-6iuj: Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iuj | |||||||||
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Title | Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus | |||||||||
Components | GH30 Xylanase B | |||||||||
Keywords | HYDROLASE / Xylanase / Glucuronoxylanase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Talaromyces cellulolyticus CF-2612 (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Nakamichi, Y. / Watanabe, M. / Inoue, H. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2019 Title: Structural and functional characterization of a bifunctional GH30-7 xylanase B from the filamentous fungusTalaromyces cellulolyticus. Authors: Nakamichi, Y. / Fouquet, T. / Ito, S. / Watanabe, M. / Matsushika, A. / Inoue, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iuj.cif.gz | 203.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iuj.ent.gz | 161.2 KB | Display | PDB format |
PDBx/mmJSON format | 6iuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iuj_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 6iuj_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 6iuj_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 6iuj_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/6iuj ftp://data.pdbj.org/pub/pdb/validation_reports/iu/6iuj | HTTPS FTP |
-Related structure data
Related structure data | 5cxpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Non-polymers , 2 types, 386 molecules AB
#1: Protein | Mass: 51575.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces cellulolyticus CF-2612 (fungus) Production host: Talaromyces cellulolyticus YP-4 (fungus) / References: UniProt: A0A4V8H018*PLUS #8: Water | ChemComp-HOH / | |
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-Sugars , 6 types, 12 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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 #7: Sugar | |
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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: 2.74 Å3/Da / Density % sol: 55.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 30% PEG 4000, 0.1 M Tris-HCl, 200 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.26 Å / Num. obs: 54785 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.25→2.28 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2649 / CC1/2: 0.819 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CXP Resolution: 2.25→48.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.176 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.483 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→48.25 Å
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Refine LS restraints |
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