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- PDB-1e6s: MYROSINASE FROM SINAPIS ALBA with bound gluco-hydroximolactam and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e6s | |||||||||
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Title | MYROSINASE FROM SINAPIS ALBA with bound gluco-hydroximolactam and sulfate | |||||||||
![]() | MYROSINASE MA1 | |||||||||
![]() | HYDROLASE / FAMILY 1 GLYCOSYL HYDROLASE / GLUCOSINOLATE / TIM BARREL / INHIBITOR / TRANSITION STATE ANALOGUE | |||||||||
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 | ![]() | 261.9 KB | Display | ![]() |
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PDB format | ![]() | 209.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.7 KB | Display | ![]() |
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Full document | ![]() | 436.9 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 1011 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e4mSC ![]() 1e6qC ![]() 1e6xC ![]() 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 , 4 types, 9 molecules ![](data/chem/img/NAG.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)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]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 / |
-Non-polymers , 5 types, 805 molecules ![](data/chem/img/GOX.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOX / ( | ||||
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#7: Chemical | ChemComp-ZN / | ||||
#8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-GOL / #10: Water | ChemComp-HOH / | |
-Details
Compound details | ACTIVE SITE NUCLEOPHILSequence details | REFERENCE: THE SEQUENCE HAS BEEN DETERMINED FROM THE X-RAY DATA. NO CORRESPONDING SEQUENCE EXISTS ...REFERENCE: THE SEQUENCE HAS BEEN DETERMINED | |
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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 PH 7.0 | ||||||||||||||||||||||||||||||||||||
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: CCD / Date: May 15, 1998 / 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: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→17.4 Å / Num. obs: 141308 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 0.7 / Rsym value: 0.337 / % possible all: 73.6 |
Reflection shell | *PLUS % possible obs: 73.6 % / Rmerge(I) obs: 0.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E4M Resolution: 1.35→10 Å / SU B: 0.568 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.045 / Details: ANISOTROPIC INDIVIDUAL B-FACTOR REFINEMENT
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Displacement parameters | Biso mean: 17.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.12 / Rfactor Rwork: 0.12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 1.42 Å / Rfactor Rfree: 0.243 / Rfactor obs: 0.186 |