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- PDB-1e6x: MYROSINASE FROM SINAPIS ALBA with a bound transition state analog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e6x | |||||||||
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Title | MYROSINASE FROM SINAPIS ALBA with a bound transition state analogue,D-glucono-1,5-lactone | |||||||||
![]() | MYROSINASE MA1 | |||||||||
![]() | HYDROLASE / FAMILY 1 GLYCOSYL HYDROLASE / GLUCOSINOLATE / TIM BARREL | |||||||||
Function / homology | ![]() thioglucosidase / thioglucosidase activity / glucosinolate glucohydrolase activity / glucosinolate catabolic process / vacuole / beta-glucosidase activity / response to salt stress / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Burmeister, W.P. | |||||||||
![]() | ![]() Title: High Resolution X-Ray Crystallography Shows that Ascorbate is a Cofactor for Myrosinase and Substitutes for the Function of the Catalytic Base Authors: Burmeister, W.P. / Cottaz, S. / Rollin, P. / Vasella, A. / Henrissat, B. #1: ![]() Title: The Crystal Structures of Sinapis Alba Myrosinase and a Covalent Glycosyl-Enzyme Intermediate Provide Insights Into the Substrate Recognition and Active-Site Machinery of an S-Glycosidase Authors: Burmeister, W.P. / Cottaz, S. / Driguez, H. / Iori, R. / Palmieri, S. / Henrissat, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.8 KB | Display | ![]() |
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PDB format | ![]() | 211 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1e4mSC ![]() 1e6qC ![]() 1e6sC ![]() 1e70C ![]() 1e71C ![]() 1e72C ![]() 1e73C 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules M
#1: Protein | Mass: 57078.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 5 types, 10 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/LGC.gif)
![](data/chem/img/LGC.gif)
#2: Polysaccharide | 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 | 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)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Polysaccharide | beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#5: Sugar | ChemComp-NAG / #6: Sugar | ChemComp-LGC / | |
-Non-polymers , 4 types, 817 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-ZN / | ||||
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#8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-GOL / #10: Water | ChemComp-HOH / | |
-Details
Compound details | ACTIVE SITE NUCLEOPHIL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 50 % / Description: ONLY THE LIGAND DIFFERS | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP METHOD, 12 MG/ML PROTEIN IN 30 MM HEPES, PH 6.5, 0.05 % NAN3 PRECIPITANT 66 % SAT. AMMONIUM SULFATE, 100MM TRIS-HCL | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging dropDetails: Burmeister, W.P., (1997) Structure (London), 5, 663. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: BENT MULTILAYER, SAGITALLY FOCUSING CRYSTAL |
Radiation | Monochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→12.1 Å / Num. obs: 99783 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.337 / % possible all: 91.3 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 91.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E4M Resolution: 1.6→10 Å / SU B: 1.2 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.069 / Details: ANISOTROPIC INDIVIDUAL B-FACTOR REFINEMENT
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Displacement parameters | Biso mean: 21.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.138 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / Rfactor Rfree: 0.286 / Rfactor obs: 0.201 |