[English] 日本語
Yorodumi- PDB-2yl9: INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yl9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS | |||||||||
Components | BETA-N-ACETYLHEXOSAMINIDASE | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Pluvinage, B. / Higgins, M.A. / Abbott, D.W. / Robb, C. / Dalia, A.B. / Deng, L. / Weiser, J.N. / Parsons, T.B. / Fairbanks, A.J. / Vocadlo, D.J. / Boraston, A.B. | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis. Authors: Pluvinage, B. / Higgins, M.A. / Abbott, D.W. / Robb, C. / Dalia, A.B. / Deng, L. / Weiser, J.N. / Parsons, T.B. / Fairbanks, A.J. / Vocadlo, D.J. / Boraston, A.B. | |||||||||
History |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yl9.cif.gz | 354.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yl9.ent.gz | 287.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yl9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yl9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2yl9_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 2yl9_validation.cif.gz | 96.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/2yl9 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2yl9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 51267.527 Da / Num. of mol.: 4 / Fragment: RESIDUES 627-1062 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49610, beta-N-acetylhexosaminidase #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 805 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 805 TO GLN ...ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97884 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97884 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→46.61 Å / Num. obs: 55642 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 88.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→40.74 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.835 / SU B: 15.098 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→40.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|