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- PDB-6kuf: Crystal structure of barley exohydrolaseI W434A mutant in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kuf | ||||||
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Title | Crystal structure of barley exohydrolaseI W434A mutant in complex with glucose. | ||||||
![]() | BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 | ||||||
![]() | HYDROLASE / Barley exohydrolaseI / enzyme function | ||||||
Function / homology | ![]() beta-glucosidase / 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 | ![]() | 257.8 KB | Display | ![]() |
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PDB format | ![]() | 203 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jg1C ![]() 6jg2C ![]() 6jg6C ![]() 6jg7C ![]() 6jgaC ![]() 6jgbC ![]() 6jgcC ![]() 6jgdC ![]() 6jgeC ![]() 6jggC ![]() 6jgkC ![]() 6jglC ![]() 6jgnC ![]() 6jgoC ![]() 6jgpC ![]() 6jgqC ![]() 6jgrC ![]() 6jgsC ![]() 6jgtC ![]() 6k6vC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65778.938 Da / Num. of mol.: 1 / Mutation: W434A 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/BGC.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Sugar | ChemComp-BGC / |
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#3: Sugar |
-Non-polymers , 4 types, 726 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ACT / | ||||
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#5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65 % |
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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 |
-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: 1.9→88.15 Å / Num. obs: 70151 / % possible obs: 99.2 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.9→1.95 Å / Rmerge(I) obs: 0.18 / Num. unique obs: 70151 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WLI Resolution: 1.9→45.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.325 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.09 Å2 / Biso mean: 29.862 Å2 / Biso min: 10.89 Å2
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Refinement step | Cycle: final / Resolution: 1.9→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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