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Yorodumi- PDB-3qef: The structure and function of an arabinan-specific alpha-1,2-arab... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qef | |||||||||
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Title | The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases | |||||||||
Components | Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N | |||||||||
Keywords | HYDROLASE / 5-bladed beta propeller | |||||||||
Function / homology | Function and homology information xylan catabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||
Biological species | Cellvibrio japonicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å | |||||||||
Authors | Cartmell, A. / Mckee, L.S. / Pena, M. / Larsbrink, J. / Brumer, H. / Lewis, R.J. / Viks-Nielsen, A. / Gilbert, H.J. / Marles-Wright, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Structure and Function of an Arabinan-specific {alpha}-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases. Authors: Cartmell, A. / McKee, L.S. / Pena, M.J. / Larsbrink, J. / Brumer, H. / Kaneko, S. / Ichinose, H. / Lewis, R.J. / Vikso-Nielsen, A. / Gilbert, H.J. / Marles-Wright, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qef.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qef.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qef_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3qef_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3qef_validation.xml.gz | 29 KB | Display | |
Data in CIF | 3qef_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/3qef ftp://data.pdbj.org/pub/pdb/validation_reports/qe/3qef | HTTPS FTP |
-Related structure data
Related structure data | 3qedSC 3qeeC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34581.766 Da / Num. of mol.: 2 / Fragment: UNP residues 28-334 / Mutation: D41A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Strain: Ueda107 / Gene: gly43N, CJA_3018 / Production host: Escherichia coli (E. coli) References: UniProt: B3PD60, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-5)]alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-5)]alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 554 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.59 Å3/Da / Density % sol: 52.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG3350, 200 mM ammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.98 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.789→44.37 Å / Num. all: 69576 / Num. obs: 69477 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.5 / Redundancy: 14.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QED Resolution: 1.789→44.367 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU ML: 0.23 / σ(F): 1.39 / Phase error: 18.71 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.207 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.789→44.367 Å
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Refine LS restraints |
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LS refinement shell |
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