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- PDB-3qee: 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: 3qee | ||||||
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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 | ![]() | 148.8 KB | Display | ![]() |
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PDB format | ![]() | 114.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qedSC ![]() 3qefC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34625.773 Da / Num. of mol.: 2 / 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 13% PEG3350, 150 mM sodium acetate, 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: Mar 16, 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: 1.64→69.635 Å / Num. all: 71594 / Num. obs: 71449 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.6 / Redundancy: 3.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QED Resolution: 1.64→69.635 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.583 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 11.394 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→69.635 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.683 Å / Total num. of bins used: 20
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