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- PDB-5glp: Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinof... -
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Open data
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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 | ||||||
![]() | Glycoside hydrolase family 43 | ||||||
![]() | HYDROLASE / Glycoside hydrolase family 43 | ||||||
Function / homology | ![]() xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matsuzawa, T. / Kishine, N. / Fujimoto, Z. / Yaoi, K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162 KB | Display | ![]() |
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PDB format | ![]() | 123 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.3 KB | Display | ![]() |
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Full document | ![]() | 465.1 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5glkC ![]() 5gllSC ![]() 5glmC ![]() 5glnC ![]() 5gloC ![]() 5glqC ![]() 5glrC 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 / Sugars , 2 types, 6 molecules AB![](data/chem/img/ARA.gif)
![](data/chem/img/ARA.gif)
#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.) ![]() Gene: coxyl43 / Plasmid: pET28b / Production host: ![]() ![]() #4: Sugar | ChemComp-ARA / |
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-Non-polymers , 4 types, 717 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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