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Yorodumi- PDB-3wkw: Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wkw | ||||||
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Title | Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum ligand free form | ||||||
Components | Non-reducing end beta-L-arabinofuranosidase | ||||||
Keywords | HYDROLASE / (alpha/alpha)6 barrel / Intracellular | ||||||
Function / homology | Function and homology information non-reducing end beta-L-arabinofuranosidase / beta-L-arabinofuranosidase activity / polysaccharide catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bifidobacterium longum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Ito, T. / Saikawa, K. / Arakawa, T. / Wakagi, T. / Fujita, K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum. Authors: Ito, T. / Saikawa, K. / Kim, S. / Fujita, K. / Ishiwata, A. / Kaeothip, S. / Arakawa, T. / Wakagi, T. / Beckham, G.T. / Ito, Y. / Fushinobu, S. #1: Journal: J.Biol.Chem. / Year: 2014 Title: Characterization of a novel beta-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member Authors: Fujita, K. / Takashi, Y. / Obuchi, E. / Kitahara, K. / Suganuma, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wkw.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wkw.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wkw_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 3wkw_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 3wkw_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 3wkw_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkw ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkw | HTTPS FTP |
-Related 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
#1: Protein | Mass: 74457.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: JCM 1217 / Gene: hypBA1 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) References: UniProt: E8MGH8, non-reducing end beta-L-arabinofuranosidase |
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#2: 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: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 0.9M sodium citrate, 0.1 M Na-cacodylate, pH 6.5, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2011 |
Radiation | Monochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 44113 / Num. obs: 44051 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rsym value: 0.075 / Net I/σ(I): 36.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 4339 / Rsym value: 0.57 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.2→40.09 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.031 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.196 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40.09 Å
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Refine LS restraints |
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