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Yorodumi- PDB-2yla: INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yla | |||||||||
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Title | INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS | |||||||||
Components | BETA-N-ACETYLHEXOSAMINIDASEHexosaminidase | |||||||||
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: 2.7 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yla.cif.gz | 352.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yla.ent.gz | 286.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/2yla ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2yla | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 49632.754 Da / Num. of mol.: 4 / 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 | Source method: isolated from a genetically manipulated source #3: 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 #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 805 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 805 TO GLN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.06 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.984 |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 55076 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2.7→29.97 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.879 / SU B: 14.058 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.597 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→29.97 Å
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Refine LS restraints |
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