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Yorodumi- PDB-4n4b: Crystal Structure of the alpha-L-arabinofuranosidase PaAbf62A fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n4b | ||||||
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Title | Crystal Structure of the alpha-L-arabinofuranosidase PaAbf62A from Podospora anserina | ||||||
Components | GH62 arabinofuranosidase | ||||||
Keywords | HYDROLASE / Beta-Propeller / hemicellulose binding | ||||||
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 | Podospora anserina (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Siguier, B. / Dumon, C. / Mourey, L. / Tranier, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: First Structural Insights into alpha-L-Arabinofuranosidases from the Two GH62 Glycoside Hydrolase Subfamilies. Authors: Siguier, B. / Haon, M. / Nahoum, V. / Marcellin, M. / Burlet-Schiltz, O. / Coutinho, P.M. / Henrissat, B. / Mourey, L. / O'Donohue, M.J. / Berrin, J.G. / Tranier, S. / Dumon, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n4b.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n4b.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n4b_validation.pdf.gz | 466.6 KB | Display | wwPDB validaton report |
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Full document | 4n4b_full_validation.pdf.gz | 471.3 KB | Display | |
Data in XML | 4n4b_validation.xml.gz | 19 KB | Display | |
Data in CIF | 4n4b_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n4b ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n4b | HTTPS FTP |
-Related structure data
Related structure data | 4n1iSC 4n2rC 4n2zC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40198.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Podospora anserina (fungus) / Strain: S Mat+ / Production host: Pichia pastoris (fungus) References: UniProt: E2GHW5, non-reducing end alpha-L-arabinofuranosidase |
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-Non-polymers , 5 types, 419 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-TRS / |
#5: Chemical | ChemComp-1PE / |
#6: 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: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 4000, 0.2M Calcium chloride 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→45 Å / Num. all: 65750 / Num. obs: 60688 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.56 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 21.86 |
Reflection shell | Resolution: 1.44→1.48 Å / Redundancy: 2 % / Mean I/σ(I) obs: 8.26 / Num. unique all: 3880 / Rsym value: 0.093 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4N1I Resolution: 1.44→44.61 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.709 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.05 / ESU R Free: 0.052 / 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: 14.643 Å2
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Refinement step | Cycle: LAST / Resolution: 1.44→44.61 Å
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Refine LS restraints |
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