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- PDB-4cte: Crystal structure of the catalytic domain of the modular laminari... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cte | |||||||||
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Title | Crystal structure of the catalytic domain of the modular laminarinase ZgLamC mutant E142S in complex with a thio-oligosaccharide | |||||||||
![]() | ENDO-1,3-BETA-GLUCANASE, FAMILY GH16 | |||||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE FAMILLY GH16 / MARINE BACTERIAL ENZYME / THIO-OLIGOSACCHARIDE COMPLEX | |||||||||
Function / homology | ![]() glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Labourel, A. / Jam, M. / Legentil, L. / Sylla, B. / Ficko-Blean, E. / Hehemann, J.H. / Ferrieres, V. / Czjzek, M. / Michel, G. | |||||||||
![]() | ![]() Title: Structural and Biochemical Characterization of the Laminarina Zglamc[Gh16] from Zobellia Galactanivorans Suggests Preferred Recognition of Branched Laminarin Authors: Labourel, A. / Jam, M. / Legentil, L. / Sylla, B. / Hehemann, J.H. / Ferrieres, V. / Czjzek, M. / Michel, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.4 KB | Display | ![]() |
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PDB format | ![]() | 165.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 34.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4crqSC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 24 - 254 / Label seq-ID: 2 - 232
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26234.705 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 23-255 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: G0L2L9, glucan endo-1,3-beta-D-glucosidase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 1-thio-beta-D-glucopyranose-(1-3)-1-thio-beta-D-glucopyranose Type: oligosaccharide / Mass: 374.427 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-glucopyranose-(1-3)-1-thio-beta-D-glucopyranose-(1-3)-1-thio-beta-D-glucopyranose Type: oligosaccharide / Mass: 536.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 7 types, 343 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | GLU 142 HAS BEEN MUTATED TO SER TO INACTIVATE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 5 Details: 11% PEG 6000, 100 MM NA ACETATE PH 5.0, 220 MM MGCL2, 4% ISOPROPANOL AND 3% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→48.2 Å / Num. obs: 72254 / % possible obs: 99.9 % / Observed criterion σ(I): 0.1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CRQ Resolution: 1.8→48.11 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.369 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 33.778 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.11 Å
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Refine LS restraints |
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