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- PDB-6jgo: Crystal structure of barley exohydrolaseI W434H mutant in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jgo | ||||||
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Title | Crystal structure of barley exohydrolaseI W434H mutant in complex with 4I,4III,4V-S-trithiocellohexaose | ||||||
![]() | BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 | ||||||
![]() | HYDROLASE / Barley exohydrolaseI / enzyme function | ||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / membrane => GO:0016020 / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luang, S. / Streltsov, V.A. / Hrmova, M. | ||||||
![]() | ![]() Title: The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Authors: Luang, S. / Fernandez-Luengo, X. / Nin-Hill, A. / Streltsov, V.A. / Schwerdt, J.G. / Alonso-Gil, S. / Ketudat Cairns, J.R. / Pradeau, S. / Fort, S. / Marechal, J.D. / Masgrau, L. / Rovira, C. / Hrmova, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.1 KB | Display | ![]() |
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PDB format | ![]() | 203.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 888.9 KB | Display | ![]() |
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Full document | ![]() | 901.5 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jg1C ![]() 6jg2C ![]() 6jg6C ![]() 6jg7C ![]() 6jgaC ![]() 6jgbC ![]() 6jgcC ![]() 6jgdC ![]() 6jgeC ![]() 6jggC ![]() 6jgkC ![]() 6jglC ![]() 6jgnC ![]() 6jgpC ![]() 6jgqC ![]() 6jgrC ![]() 6jgsC ![]() 6jgtC ![]() 6k6vC ![]() 6kufC ![]() 6l1jC ![]() 6lbbC ![]() 6lbvC ![]() 6lc5C ![]() 3wliS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65846.000 Da / Num. of mol.: 1 / Mutation: W434H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose / thio-beta-cellobiose |
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#3: Sugar |
-Non-polymers , 5 types, 640 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | Lys320 is confirmed by DNA sequencing result. However, the electron density map is not clear, ...Lys320 is confirmed by DNA sequencing result. However, the electron density map is not clear, probably side chain of this residue is flexible. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2012 / Details: COLLIMATING MIRROR |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→87.8 Å / Num. obs: 64595 / % possible obs: 99.9 % / Redundancy: 29 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.847 / Num. unique obs: 125703 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WLI Resolution: 1.95→48.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.142 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.653 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→48.38 Å
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Refine LS restraints |
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