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- PDB-5gy0: Crystal structure of endoglucanase CelQ from Clostridium thermoce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gy0 | ||||||||||||
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Title | Crystal structure of endoglucanase CelQ from Clostridium thermocellum complexed with cellotetraose | ||||||||||||
![]() | Glucanase![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() 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 | ![]() | 538.9 KB | Display | ![]() |
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PDB format | ![]() | 435.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5gxxC ![]() 5gxyC ![]() 5gxzC ![]() 5gy1C ![]() 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: 69154.562 Da / Num. of mol.: 2 / Fragment: UNP residues 28-629 / Mutation: I251T, E435A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9AJF8, ![]() #2: Polysaccharide | |
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-Non-polymers , 5 types, 1419 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / ![]() #5: Chemical | ChemComp-BR / | ![]() #6: Chemical | ChemComp-PG4 / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 9-12%(w/v) PEG3350, 15-20%(v/v) PEG550MME, 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 210r / Detector: CCD / Date: Dec 18, 2012 Details: Vertically Collimating Premirror, Toroidal Focusing Mirror |
Radiation | Monochromator: Fixed-Exit Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.74→30 Å / Num. obs: 167086 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.74→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1GA2 Resolution: 1.74→22.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.874 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086 / 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: 22.872 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→22.94 Å
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Refine LS restraints |
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