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Yorodumi- PDB-2yl6: Inhibition of the pneumococcal virulence factor StrH and molecula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yl6 | ||||||
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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 / PEPTIDOGLYCAN-ANCHOR | ||||||
Function / homology | Function and homology information beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 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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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yl6.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yl6.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/2yl6 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2yl6 | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 48207.746 Da / Num. of mol.: 1 / Fragment: RESIDUES 181-614 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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-ETE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.93 Å / Num. obs: 59835 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.6→19.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.103 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 18.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.83 Å
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Refine LS restraints |
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