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- PDB-5a8n: Crystal structure of the native form of beta-glucanase SdGluc5_26... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a8n | ||||||
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Title | Crystal structure of the native form of beta-glucanase SdGluc5_26A from Saccharophagus degradans | ||||||
![]() | PUTATIVE RETAINING B-GLYCOSIDASE | ||||||
![]() | HYDROLASE / CAZYME / GLYCOSIDE HYDROLASE / SACCHAROPHAGUS DEGRADANS / 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 | ![]() | 156.1 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 457.9 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a8mSC ![]() 5a8oC ![]() 5a8pC ![]() 5a8qC ![]() 5a94C ![]() 5a95C S: Starting model for refinement C: citing same article ( |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 42096.664 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 6 types, 316 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Chemical | ChemComp-PGE / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.7 % / 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: Feb 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→32.8 Å / Num. obs: 32184 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 29.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: WWPDB ENTRY 5A8M Resolution: 2.05→32.91 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.454 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.12 / 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: 31.695 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→32.91 Å
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Refine LS restraints |
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