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Yorodumi- PDB-1w9d: S. alba myrosinase in complex with S-ethyl phenylacetothiohydroxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w9d | |||||||||
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Title | S. alba myrosinase in complex with S-ethyl phenylacetothiohydroximate- O-sulfate | |||||||||
Components | GLYCOSIDASE | |||||||||
Keywords | HYDROLASE / THIOGLUCOSIDASE / THIOGLYCOSIDASE / MYROSINASE / THIO-GLUCOSIDE / THIOHYDROXIMATE / GLUSOSINOLATE / GLUCOTROPAEOLIN | |||||||||
Function / homology | Function and homology information 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 | SINAPIS ALBA (white mustard) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Bourderioux, A. / Lefoix, M. / Gueyrard, D. / Tatibouet, A. / Cottaz, S. / Arzt, S. / Burmeister, W.P. / Rollin, P. | |||||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2005 Title: The Glucosinolate-Myrosinase System. New Insights Into Enzyme-Substrate Interactions by Use of Simplified Inhibitors Authors: Bourderioux, A. / Lefoix, M. / Gueyrard, D. / Tatibouet, A. / Cottaz, S. / Arzt, S. / Burmeister, W.P. / Rollin, P. #1: Journal: J.Biol.Chem. / Year: 2000 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. | |||||||||
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 | 1w9d.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9d.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 1w9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9d ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9d | HTTPS FTP |
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-Related structure data
Related structure data | 1w9bC 1e4mS C: citing same article (ref.) 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) / Organ: SEED / Strain: EMERGO / Tissue: MYROSIN GRAINS / References: UniProt: P29736*PLUS, EC: 3.2.3.1 |
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-Sugars , 4 types, 10 molecules
#2: Polysaccharide | 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, 770 molecules
#6: Chemical | ChemComp-SEH / | ||||
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#7: Chemical | ChemComp-ZN / | ||||
#8: Chemical | ChemComp-SO4 / #9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Sequence details | OUR SEQUENCE IS AN X-RAY SEQUENCE BASED ON THE ASSIGNMENT OF THE RESIDUES BY THEIR ELECTRON DENSITY. ...OUR SEQUENCE IS AN X-RAY SEQUENCE BASED ON THE ASSIGNMENT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 50 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 27, 2002 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND 111 AND SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→35 Å / Num. obs: 146755 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.4 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E4M Resolution: 1.6→35 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: INHIBITOR TOPOLOGY AND PARAMETERS SAME AS IN ENTRY 1W9B, ONLY MOST OF THE ATOMS OF THE GLUCOSE GROUP HAVE BEEN DELETED. THE INHIBITOR HAS BEEN RENAMED FROM CGT TO SEH AFTER REFINEMENT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9271 Å2 / ksol: 0.380436 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
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Xplor file |
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