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- PDB-3wlk: Crystal structure of barley beta-D-glucan glucohydrolase isoenzym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wlk | |||||||||
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Title | Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme EXO1 in complex with 4-deoxy-glucose | |||||||||
![]() | Beta-D-glucan exohydrolase isoenzyme ExoI | |||||||||
![]() | HYDROLASE / BETA BARREL / GRAIN DEVELOPMENT / Enzyme Function Initiative / Tim Barrel/Beta sheet / N-glycosylation / plant apoplast | |||||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Streltsov, V.A. / Hrmova, M. | |||||||||
![]() | ![]() Title: Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / ...Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / Mendoza, F. / Tiessler-Sala, L. / Sanchez-Aparicio, J.E. / Rodriguez-Guerra, J. / Lluch, J.M. / Marechal, J.D. / Masgrau, L. / 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 | ![]() | 264.1 KB | Display | ![]() |
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PDB format | ![]() | 209.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wlhC ![]() 3wliC ![]() 3wljC ![]() 3wllC ![]() 3wlmC ![]() 3wlnC ![]() 3wloC ![]() 3wlpC ![]() 3wlqC ![]() 3wlrC ![]() 6md6C ![]() 6mi1C ![]() 1ieqS ![]() 3wlt 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 X
#1: Protein | Mass: 65475.617 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-630 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q9XEI3, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Sugars , 4 types, 4 molecules ![](data/chem/img/BGC.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-BGC / |
-Non-polymers , 3 types, 887 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING OF AF102868 (GENBANK ACCESSION NUMBER). ...THE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 75mM HEPES-NaOH pH7.0 buffer, 1.2% PEG 400, 1.7M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 12, 2005 / Details: RH COATED SI MIRROR |
Radiation | Monochromator: C(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→88.05 Å / Num. all: 88188 / Num. obs: 88188 / % possible obs: 99.5 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.3 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IEQ Resolution: 1.8→88.05 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.527 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.084 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.961 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→88.05 Å
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Refine LS restraints |
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