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Yorodumi- PDB-3wp3: Xylanase 11C from Talaromyces cellulolyticus (formerly known as A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wp3 | ||||||
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Title | Xylanase 11C from Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) | ||||||
Components | Endo-1,4-beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / Beta-jelly roll / Glycoside hydrolase | ||||||
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 | Talaromyces funiculosus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Ishikawa, K. / Inoue, H. / Kataoka, M. | ||||||
Citation | Journal: Appl Biochem Biotechnol. / Year: 2014 Title: Crystal structure of Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) GH family 11 xylanase Authors: Kataoka, M. / Akita, F. / Maeno, Y. / Inoue, B. / Inoue, H. / Ishikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wp3.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wp3.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wp3 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wp3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22495.115 Da / Num. of mol.: 2 / Fragment: UNP residues 28-207 / Mutation: D59N, P85T, S121L, N141D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces funiculosus (fungus) / Gene: xynC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HFH0, endo-1,4-beta-xylanase #2: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 56.98 % / Mosaicity: 0.599 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.8M Sodium dihydrogen phosphate, 0.8M Potassium dihydrogen phosphate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 17, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. obs: 35412 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.108 / Χ2: 1.061 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2687 / WRfactor Rwork: 0.2288 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.801 / SU B: 3.804 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1819 / SU Rfree: 0.1713 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.71 Å2 / Biso mean: 25.7715 Å2 / Biso min: 6.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.032 Å / Total num. of bins used: 20
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