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Yorodumi- PDB-2wxd: A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wxd | |||||||||
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Title | A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE | |||||||||
Components | MYROSINASE | |||||||||
Keywords | HYDROLASE / VACUOLE / THIOHYDROXIMATE / GLUCOSINOLATE / FAMILY 1 GLYCOSYL HYDROLASE / GLYCOSIDASE / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information thioglucosidase / thioglucosidase activity / : / glucosinolate catabolic process / vacuole / beta-glucosidase activity / response to salt stress / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | SINAPIS ALBA (white mustard) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Besle, A. / Burmeister, W.P. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: A Micromolar O-Sulfated Thiohydroximate Inhibitor Bound to Plant Myrosinase Authors: Besle, A. / Brazzolotto, X. / Tatibouet, A. / Cerniauskaite, D. / Gallienne, E. / Rollin, P. / Burmeister, W.P. #1: Journal: Tetrahedron Letters / Year: 2009 Title: A Simple O-Sulfated Thiohydroximate Molecule to be the First Micromolar Range Myrosinase Inhibitor Authors: Cerniauskaite, D. / Gallienne, E. / Karciauskaite, H. / Farinha, A.S.F. / Rousseau, J. / Armand, S. / Tatibouet, A. / Sackus, A. / Rollin, P. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wxd.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wxd.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wxd_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 2wxd_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 2wxd_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 2wxd_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/2wxd ftp://data.pdbj.org/pub/pdb/validation_reports/wx/2wxd | HTTPS FTP |
-Related structure data
Related structure data | 1e4mS S: Starting model for refinement |
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Similar structure data |
-Links
-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) SINAPIS ALBA (white mustard) / Strain: EMERGO / References: UniProt: P29736, EC: 3.2.3.1 |
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-Sugars , 4 types, 10 molecules
#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 #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 / |
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-Non-polymers , 5 types, 777 molecules
#6: Chemical | ChemComp-E18 / | ||||
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#7: Chemical | ChemComp-ZN / | ||||
#8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-GOL / #10: Water | ChemComp-HOH / | |
-Details
Has protein modification | Y | ||
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Nonpolymer details | S-(N,N-DIMETHYLAMSequence details | SEQUENCE OBTAINED FROM ELECTRON DENSITY OF THE XRAY STRUCTURE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 43 % / Description: ISOMORPHOUS TO 1E4M |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: TRIS-HCL PH 8, 68 % SAT AMMONIUM SULFATE; PROTEIN IN HEPES PH 6.5, 150 MM NACL, 0.02 MM ZNSO4; HANGING DROPS 2 AND 2 UL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 18, 2008 |
Radiation | Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→80.85 Å / Num. obs: 99631 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.63 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.71 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E4M Resolution: 1.6→68.78 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.004 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 12.436 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→68.78 Å
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Refine LS restraints |
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