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Yorodumi- PDB-2wmh: Crystal structure of the catalytic module of a family 98 glycosid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wmh | |||||||||
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Title | Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae TIGR4 in complex with the H- disaccharide blood group antigen. | |||||||||
Components | FUCOLECTIN-RELATED PROTEIN | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / STREPTOCOCCUS PNEUMONIAE / BLOOD GROUP ANTIGEN / FUCOSE UTILIZATION | |||||||||
Function / homology | Function and homology information regulation of complement activation, lectin pathway / regulation of cellular defense response / fucose binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å | |||||||||
Authors | Higgins, M.A. / Whitworth, G.E. / El Warry, N. / Randriantsoa, M. / Samain, E. / Burke, R.D. / Vocadlo, D.J. / Boraston, A.B. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Differential Recognition and Hydrolysis of Host Carbohydrate-Antigens by Streptococcus Pneumoniae Family 98 Glycoside Hydrolases. Authors: Higgins, M.A. / Whitworth, G.E. / El Warry, N. / Randriantsoa, M. / Samain, E. / Burke, R.D. / 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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | 2wmh.cif.gz | 250.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wmh.ent.gz | 202.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/2wmh ftp://data.pdbj.org/pub/pdb/validation_reports/wm/2wmh | 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
#1: Protein | Mass: 66785.688 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 31-589 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q97N96, UniProt: A0A0H2US34*PLUS |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.45 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Type: NSLS / Wavelength: 1.1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 55648 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.9 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.7→19.43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.159 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.105 / 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: 8.571 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.43 Å
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Refine LS restraints |
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