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- PDB-5a8q: Crystal structure beta-glucanase SdGluc5_26A from Saccharophagus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a8q | |||||||||
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Title | Crystal structure beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A obtained by soaking | |||||||||
![]() | PUTATIVE RETAINING B-GLYCOSIDASE | |||||||||
![]() | HYDROLASE / CAZYME / GLYCOSIDE HYDROLASE / BETA-GLUCANASE / GH5_26 | |||||||||
Function / homology | ![]() glucan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sulzenbacher, G. / Lafond, M. / Freyd, T. / Henrissat, B. / Coutinho, R.M. / Berrin, J.G. / Garron, M.L. | |||||||||
![]() | ![]() Title: The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans Authors: Lafond, M. / Sulzenbacher, G. / Freyd, T. / Henrissat, B. / Berrin, J.G. / Garron, M.L. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.2 KB | Display | ![]() |
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PDB format | ![]() | 126.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.8 KB | Display | ![]() |
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Full document | ![]() | 786.3 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a8mC ![]() 5a8nC ![]() 5a8oSC ![]() 5a8pC ![]() 5a94C ![]() 5a95C 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 42095.680 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-365 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 7 types, 428 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GXT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GXT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / | ||
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#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | ChemComp-GOL / | ||
#6: Chemical | ChemComp-PGE / | ||
#7: Chemical | ChemComp-GXT / | ||
#8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.5 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM CACODYLATE BUFFER PH 6.0, 25% (W/V) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.9 Å / Num. obs: 40497 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 17.94 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5A8O Resolution: 1.9→47.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.431 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 18.073 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.95 Å
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Refine LS restraints |
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