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- PDB-5a8m: Crystal structure of the selenomethionine derivative of beta-gluc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a8m | ||||||
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Title | Crystal structure of the selenomethionine derivative of beta-glucanase SdGluc5_26A from Saccharophagus degradans | ||||||
![]() | 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" 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 | ![]() | 439.1 KB | Display | ![]() |
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PDB format | ![]() | 375.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.7 KB | Display | ![]() |
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Full document | ![]() | 486.2 KB | Display | |
Data in XML | ![]() | 50.1 KB | Display | |
Data in CIF | ![]() | 76.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a8nC ![]() 5a8oC ![]() 5a8pC ![]() 5a8qC ![]() 5a94C ![]() 5a95C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 42424.930 Da / Num. of mol.: 3 / 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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-Non-polymers , 6 types, 1267 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 | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #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: 2.94 Å3/Da / Density % sol: 58.2 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 25% (W/V) PEG3350, 0.2 M MGCL2, 0.1 M BIS-TRIS BUFFER PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→47.53 Å / Num. obs: 116426 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.5 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.86→47.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.598 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.094 / 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: 18.061 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→47.33 Å
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Refine LS restraints |
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