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Yorodumi- PDB-3a23: Crystal Structure of beta-L-Arabinopyranosidase complexed with D-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a23 | ||||||
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Title | Crystal Structure of beta-L-Arabinopyranosidase complexed with D-galactose | ||||||
Components | Putative secreted alpha-galactosidase | ||||||
Keywords | HYDROLASE / beta-alpha-barrel / Greek key motif / beta-jellyroll / beta-trefoil | ||||||
Function / homology | Function and homology information alpha-galactosidase / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Fujimoto, Z. / Ichinose, H. / Kaneko, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27. Authors: Ichinose, H. / Fujimoto, Z. / Honda, M. / Harazono, K. / Nishimoto, Y. / Uzura, A. / Kaneko, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary crystallographic analysis of exo-alpha-1,5-L-arabinofuranosidase from Streptomyces avermitilis NBRC14893. Authors: Fujimoto, Z. / Ichinose, H. / Kaneko, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a23.cif.gz | 276.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a23.ent.gz | 218.7 KB | Display | PDB format |
PDBx/mmJSON format | 3a23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/3a23 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/3a23 | HTTPS FTP |
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-Related structure data
Related structure data | 3a21SC 3a22C 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 64307.629 Da / Num. of mol.: 2 / Fragment: UNP residues 45-658 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: NBRC14893 / Gene: agaA2, SAV2186, SAV_2186 / Plasmid: pIJ702 / Production host: Streptomyces lividans (bacteria) / Strain (production host): 1326 / References: UniProt: Q82L26 #2: Sugar | |
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-Non-polymers , 5 types, 1514 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EPE / | #7: 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: 2.39 Å3/Da / Density % sol: 48.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.7M ammonium sulfate, 1.7% PEG 400, 15% glycerol, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 97694 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 9.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A21 Resolution: 1.9→41.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.199 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.117 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→41.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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