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- PDB-6yon: Crystal structure of Endoglucanase S127C/A165C from Penicillium v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yon | ||||||
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Title | Crystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum | ||||||
![]() | Endoglucanase | ||||||
![]() | HYDROLASE / ENDOHYDROLYSIS / CELLULOSE | ||||||
Function / homology | Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / cellulase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum Authors: Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.2 KB | Display | ![]() |
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PDB format | ![]() | 197.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 44.8 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i6sS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34693.934 Da / Num. of mol.: 4 / Mutation: S127C/A165C Source method: isolated from a genetically manipulated source Details: ANSKEVKKRASSFEWFGSNESGAEFGSGNIPGVEGTDYTFPNTTAIQILIDAGMNIFRVPFLMERMIPTEMTGSLDTAYF EGYSEVINYITGKGAHAVVDPHNFGRYYGTPISSTSDFQTFWSTLASQFKSNDLVIFDTNNEYHDMDESVVVALNQAAID ...Details: ANSKEVKKRASSFEWFGSNESGAEFGSGNIPGVEGTDYTFPNTTAIQILIDAGMNIFRVPFLMERMIPTEMTGSLDTAYF EGYSEVINYITGKGAHAVVDPHNFGRYYGTPISSTSDFQTFWSTLASQFKSNDLVIFDTNNEYHDMDESVVVALNQAAID GIRDAGATTQYIFVEGNAYSGAWTWTTYNTAMVNLTDPSDLIVYEMHQYLDSAGSGTSDQCVSSTVGQERVVDATTWLQS NGKLGILGEFAGGANSVCEEAVEGMLDYLAENSDVWLGASWWSAGPWWQDYIYSMEPPNGIAYESYLSILETYF Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG 6000,Bis-Tris-Propane, MPD, tert-butanol |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2019 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.978565037251 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→49.34 Å / Num. obs: 48284 / % possible obs: 99.24 % / Redundancy: 4.08 % / CC1/2: 0.994 / Net I/σ(I): 5.15 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.46 Å / Num. unique obs: 3354 / CC1/2: 0.683 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I6S Resolution: 2.6→49.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 12.569 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.506 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→49.34 Å
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Refine LS restraints |
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