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Yorodumi- PDB-4n2r: Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n2r | |||||||||
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Title | Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maydis in complex with L-arabinofuranose | |||||||||
Components | alpha-L-arabinofuranosidase UmAbf62A | |||||||||
Keywords | HYDROLASE / Beta-Propeller / hemicellulose binding | |||||||||
Function / homology | Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Mainly Beta / alpha-L-arabinofuranose / beta-L-arabinofuranose / : Function and homology information | |||||||||
Biological species | Ustilago maydis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 4n2r.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n2r.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 4n2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n2r_validation.pdf.gz | 478.4 KB | Display | wwPDB validaton report |
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Full document | 4n2r_full_validation.pdf.gz | 483.9 KB | Display | |
Data in XML | 4n2r_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4n2r_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/4n2r ftp://data.pdbj.org/pub/pdb/validation_reports/n2/4n2r | HTTPS FTP |
-Related structure data
Related structure data | 4n1iSC 4n2zC 4n4bC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37054.156 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (fungus) / Strain: 521/FGSC 9021 / Gene: UM04309.1 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) References: UniProt: Q4P6F4, non-reducing end alpha-L-arabinofuranosidase |
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-Sugars , 2 types, 2 molecules
#3: Sugar | ChemComp-FUB / |
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#4: Sugar | ChemComp-AHR / |
-Non-polymers , 3 types, 440 molecules
#2: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-TRS / |
#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: 1.82 Å3/Da / Density % sol: 32.56 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% (w/v) PEG 3350 0.2 M Sodium phosphate 0.05 M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2012 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 85293 / Num. obs: 81763 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.026 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 9.35 / Num. unique all: 5597 / Rsym value: 0.143 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4N1I Resolution: 1.2→47.42 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.743 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.03 / ESU R Free: 0.032 / 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: 10.908 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→47.42 Å
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Refine LS restraints |
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