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- PDB-6jg7: Crystal structure of barley exohydrolaseI W286F in complex with m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jg7 | ||||||
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Title | Crystal structure of barley exohydrolaseI W286F in complex with methyl 2-thio-beta-sophoroside | ||||||
![]() | 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 | ![]() | 251.8 KB | Display | ![]() |
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PDB format | ![]() | 197.9 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 | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jg1C ![]() 6jg2C ![]() 6jg6C ![]() 6jgaC ![]() 6jgbC ![]() 6jgcC ![]() 6jgdC ![]() 6jgeC ![]() 6jggC ![]() 6jgkC ![]() 6jglC ![]() 6jgnC ![]() 6jgoC ![]() 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: 65855.031 Da / Num. of mol.: 1 / Mutation: W286F 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-(1-2)-methyl 2-thio-beta-D-glucopyranoside / METHYL 2-THIO-BETA-SOPHOROSIDE |
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#3: Sugar |
-Non-polymers , 4 types, 432 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.47 % |
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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: 2.16→87.68 Å / Num. obs: 47914 / % possible obs: 99.8 % / Redundancy: 29 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 46.7 |
Reflection shell | Resolution: 2.16→2.21 Å / Rmerge(I) obs: 0.133 / Num. unique obs: 3421 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WLI Resolution: 2.16→87.68 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.187 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 109.81 Å2 / Biso mean: 26.659 Å2 / Biso min: 10.57 Å2
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Refinement step | Cycle: final / Resolution: 2.16→87.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.213 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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