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Open data
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Basic information
Entry | Database: PDB / ID: 5jx5 | ||||||
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Title | GH6 Orpinomyces sp. Y102 enzyme | ||||||
![]() | Glucanase | ||||||
![]() | HYDROLASE / Orpinomyces sp. / GH6 / Cbh7 / endoglucanases / exoglucanases | ||||||
Function / homology | ![]() Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tsai, L.C. / Huang, H.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo- and endo- activity in a complex with cellobiose Authors: Huang, H.C. / Qi, L.H. / Chen, Y.C. / Tsai, L.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 281.9 KB | Display | ![]() |
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PDB format | ![]() | 235.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 543 KB | Display | ![]() |
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Full document | ![]() | 586.9 KB | Display | |
Data in XML | ![]() | 66.5 KB | Display | |
Data in CIF | ![]() | 95.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35438.246 Da / Num. of mol.: 4 / Fragment: UNP residues 128-449 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A076U926, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Non-polymers , 8 types, 1137 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / | ||||||||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NH4 / #6: Chemical | ChemComp-MPD / ( | #7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 6K, 0.1M ammonium phosphate buffer, 2% MPD |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. obs: 200111 / % possible obs: 98.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 / Net I/av σ(I): 23.809 / Net I/σ(I): 20.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Resolution: 1.8→27.76 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.107 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 92.88 Å2 / Biso mean: 31.986 Å2 / Biso min: 13.14 Å2
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Refinement step | Cycle: final / Resolution: 1.8→27.76 Å
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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