[English] 日本語
Yorodumi- PDB-1e72: Myrosinase from Sinapis alba with bound gluco-hydroximolactam and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+72 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Myrosinase from Sinapis alba with bound gluco-hydroximolactam and sulfate or ascorbate | ||||||||||||
Components | MYROSINASE MA1 | ||||||||||||
Keywords | HYDROLASE / FAMILY 1 GLYCOSYL HYDROLASE / GLUCOSINOLATE / TIM BARREL / ACTIVATION / INHIBITOR / TRANSITION STATE ANALOGUE | ||||||||||||
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 | Burmeister, W.P. | ||||||||||||
Citation | 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. #1: Journal: Structure / Year: 1997 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1e72.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1e72.ent.gz | 209.4 KB | Display | PDB format |
PDBx/mmJSON format | 1e72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e72_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1e72_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1e72_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 1e72_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/1e72 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/1e72 | HTTPS FTP |
-Related structure data
Related structure data | 1e4mSC 1e6qC 1e6sC 1e6xC 1e70C 1e71C 1e73C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-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) / Cellular location: MYROSIN GRAINS / Organ: SEED / Strain: EMERGO / References: UniProt: P29736, EC: 3.2.3.1 |
---|
-Sugars , 5 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)]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-ASC / | |
-Non-polymers , 5 types, 801 molecules
#7: Chemical | ChemComp-GOX / ( | ||||
---|---|---|---|---|---|
#8: Chemical | ChemComp-ZN / | ||||
#9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-GOL / #11: Water | ChemComp-HOH / | |
-Details
Compound details | ACTIVE SITE NUCLEOPHILE: GLU409 AT THE POSITION OF THE GENERAL ACID/BASE: GLN187 THERE ARE ...ACTIVE SITE NUCLEOPHIL |
---|---|
Sequence details | REFERENCE: THE SEQUENCE HAS BEEN DETERMINED FROM THE X-RAY DATA. THE 2 N-TERMINAL RESIDUES HAVE ...REFERENCE: THE SEQUENCE HAS BEEN DETERMINED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 50 % / Description: ONLY THE LIGAND DIFFERS | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.948 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 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: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.3 Å / Num. obs: 110239 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2 / Rsym value: 0.256 / % possible all: 99.7 |
Reflection | *PLUS Num. obs: 84662 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 99.7 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E4M Resolution: 1.6→10 Å / SU B: 0.96 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.062 / Details: ANISOTROPIC INDIVIDUAL B-FACTOR REFINEMENT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.129 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / Rfactor Rfree: 0.198 / Rfactor obs: 0.163 |