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Yorodumi- PDB-4pva: Crystal structure of GH62 hydrolase from thermophilic fungus Scyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pva | ||||||
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Title | Crystal structure of GH62 hydrolase from thermophilic fungus Scytalidium thermophilum | ||||||
Components | GH62 hydrolase | ||||||
Keywords | HYDROLASE / Arabinofuranosidase / arabinofuranohydrolase / GH62 hydrolase / fungal genomics / arabinoxylan / lignocellulose degradation | ||||||
Function / homology | Function and homology information L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Scytalidium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å | ||||||
Authors | Nocek, B. / Kaur, A.P. / Xu, X. / Cui, H. / Savchenko, A. | ||||||
Citation | Journal: Microb Biotechnol / Year: 2015 Title: Functional and structural diversity in GH62 alpha-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum. Authors: Kaur, A.P. / Nocek, B.P. / Xu, X. / Lowden, M.J. / Leyva, J.F. / Stogios, P.J. / Cui, H. / Di Leo, R. / Powlowski, J. / Tsang, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pva.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pva.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/4pva ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pva | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 39198.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scytalidium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059U759*PLUS | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 2.2 M ammonium di-hydrate phosphate, 12% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→28 Å / Num. all: 103224 / Num. obs: 97754 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.23→1.25 Å / % possible all: 52.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.23→27.49 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.17 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.04 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.531 Å2
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Refinement step | Cycle: LAST / Resolution: 1.23→27.49 Å
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Refine LS restraints |
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