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- PDB-3a21: Crystal Structure of Streptomyces avermitilis beta-L-Arabinopyran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a21 | ||||||
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Title | Crystal Structure of Streptomyces avermitilis beta-L-Arabinopyranosidase | ||||||
![]() | Putative secreted alpha-galactosidase | ||||||
![]() | HYDROLASE / beta-alpha-barrel / Greek key motif / beta-jellyroll / beta-trefoil | ||||||
Function / homology | ![]() alpha-galactosidase / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujimoto, Z. / Ichinose, H. / Kaneko, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.4 KB | Display | ![]() |
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PDB format | ![]() | 229 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 61.1 KB | Display | |
Data in CIF | ![]() | 97.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a22C ![]() 3a23C ![]() 1uasS ![]() 1xyfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 , 1 types, 2 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.) ![]() ![]() |
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-Non-polymers , 5 types, 1865 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/1PG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-1PG / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.26 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 191711 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 6.5 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UAS, 1XYF Resolution: 1.51→33.37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.987 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / 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: 13.457 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.51→33.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.506→1.545 Å / Total num. of bins used: 20
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