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- PDB-5gy1: Crystal structure of endoglucanase CelQ from Clostridium thermoce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gy1 | ||||||||||||
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Title | Crystal structure of endoglucanase CelQ from Clostridium thermocellum complexed with cellotriose | ||||||||||||
![]() | Glucanase | ||||||||||||
![]() | HYDROLASE / CELLULASES / GLYCOSYL HYDROLASE / CELLULOSOME | ||||||||||||
Function / homology | ![]() Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Jeng, W.Y. / Liu, C.I. / Wang, A.H.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of the C-Terminally Truncated Endoglucanase Cel9Q from Clostridium thermocellum Complexed with Cellodextrins and Tris. Authors: Jeng, W.Y. / Liu, C.I. / Lu, T.J. / Lin, H.J. / Wang, N.C. / Wang, A.H. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 513 KB | Display | ![]() |
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PDB format | ![]() | 415.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 50.8 KB | Display | |
Data in CIF | ![]() | 76.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gxxC ![]() 5gxyC ![]() 5gxzC ![]() 5gy0C ![]() 1ga2S 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 69168.586 Da / Num. of mol.: 2 / Fragment: UNP residues 28-629 / Mutation: D79A, I251T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9AJF8, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Polysaccharide | |
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-Non-polymers , 4 types, 925 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-BR / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 9-12%(w/v) PEG 3350, 15-20%(v/v) PEG 550MME, 30mM NaBr, 30mM NaF and 30mM NaI, 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2013 Details: Vertically Collimating Premirror, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. obs: 108829 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GA2 Resolution: 1.99→25.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.76 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.898 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→25.94 Å
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Refine LS restraints |
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