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Yorodumi- PDB-5glp: Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinof... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5glp | ||||||
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Title | Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose, calcium-bound form | ||||||
Components | Glycoside hydrolase family 43 | ||||||
Keywords | HYDROLASE / Glycoside hydrolase family 43 | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Matsuzawa, T. / Kishine, N. / Fujimoto, Z. / Yaoi, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J. Biochem. / Year: 2017 Title: Crystal structure of metagenomic beta-xylosidase/ alpha-l-arabinofuranosidase activated by calcium. Authors: Matsuzawa, T. / Kaneko, S. / Kishine, N. / Fujimoto, Z. / Yaoi, K. #1: Journal: Appl. Microbiol. Biotechnol. / Year: 2015 Title: Screening, identification, and characterization of a GH43 family beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome. Authors: Matsuzawa, T. / Kaneko, S. / Yaoi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5glp.cif.gz | 162 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5glp.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 5glp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/5glp ftp://data.pdbj.org/pub/pdb/validation_reports/gl/5glp | HTTPS FTP |
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-Related structure data
Related structure data | 5glkC 5gllSC 5glmC 5glnC 5gloC 5glqC 5glrC C: citing same article (ref.) S: Starting model for refinement |
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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 / Sugars , 2 types, 6 molecules AB
#1: Protein | Mass: 38529.520 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 47-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: coxyl43 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H5BL38 #4: Sugar | ChemComp-ARA / |
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-Non-polymers , 4 types, 717 molecules
#2: Chemical | #3: Chemical | #5: Chemical | ChemComp-ACT / | #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: 2.49 Å3/Da / Density % sol: 50.7 % / Description: Plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% PEG 3350, 8% Tacsimate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 25, 2015 |
Radiation | Monochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. obs: 66300 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.649 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.4 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GLL Resolution: 1.8→78.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.009 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.099 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.221 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→78.71 Å
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Refine LS restraints |
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