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- PDB-3qed: The structure and function of an arabinan-specific alpha-1,2-arab... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qed | ||||||
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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 | ||||||
![]() | Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N | ||||||
![]() | HYDROLASE / 5-bladed beta propeller | ||||||
Function / homology | ![]() Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cartmell, A. / Mckee, L.S. / Pena, M. / Larsbrink, J. / Brumer, H. / Lewis, R.J. / Viks-Nielsen, A. / Gilbert, H.J. / Marles-Wright, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.1 KB | Display | ![]() |
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PDB format | ![]() | 210.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.9 KB | Display | ![]() |
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Full document | ![]() | 516.1 KB | Display | |
Data in XML | ![]() | 43.3 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35686.719 Da / Num. of mol.: 4 / Fragment: UNP residues 28-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B3PD60, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-TAM / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M ammonium sulfate, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→72.17 Å / Num. obs: 50829 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Rmerge(I) obs: 0.215 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.99→3.15 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() 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 mean: 22.937 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→72.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.068 Å / Total num. of bins used: 20
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