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- PDB-6l1j: 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: 6l1j | ||||||
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Title | Crystal structure of barley exohydrolaseI W434A mutant in complex with 4'-nitrophenyl thiolaminaritrioside | ||||||
![]() | 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 | ![]() | 258.4 KB | Display | ![]() |
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PDB format | ![]() | 203 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 49.2 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 ![]() 6jgoC ![]() 6jgpC ![]() 6jgqC ![]() 6jgrC ![]() 6jgsC ![]() 6jgtC ![]() 6k6vC ![]() 6kufC ![]() 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 / Sugars , 2 types, 4 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#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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#2: Sugar |
-Non-polymers , 6 types, 702 molecules ![](data/chem/img/LAM.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-LAM / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-1PE / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Sequence details | Amino acid at the position 320 should be Lysine. However, the electron density map is not clear, ...Amino acid at the position 320 should be Lysine. 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: 3.52 Å3/Da / Density % sol: 65.07 % |
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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: 1.8→88.23 Å / Num. obs: 83048 / % possible obs: 99.8 % / Redundancy: 26.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 51.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.055 / Num. unique obs: 6011 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WLI Resolution: 1.8→27.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.846 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.077 / 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: 93.48 Å2 / Biso mean: 23.809 Å2 / Biso min: 12.56 Å2
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Refinement step | Cycle: final / Resolution: 1.8→27.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 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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