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Yorodumi- PDB-2wmi: Crystal structure of the catalytic module of a family 98 glycosid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wmi | |||||||||
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Title | Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae SP3-BS71 in complex with the A-trisaccharide blood group antigen. | |||||||||
Components | (FUCOLECTIN-RELATED PROTEIN) x 2 | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / FUCOSE UTILIZATION / BLOOD GROUP ANTIGEN | |||||||||
Function / homology | Function and homology information family 98 glycoside hydrolase / arginine biosynthesis bifunctional protein fold / Polysaccharide lyase family 8-like, C-terminal / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 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. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 | 2wmi.cif.gz | 268.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wmi.ent.gz | 213 KB | Display | PDB format |
PDBx/mmJSON format | 2wmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wmi_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2wmi_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2wmi_validation.xml.gz | 52.5 KB | Display | |
Data in CIF | 2wmi_validation.cif.gz | 79.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/2wmi ftp://data.pdbj.org/pub/pdb/validation_reports/wm/2wmi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 69895.352 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 422-1005 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: SP3-BS71 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: A5LBQ0 | ||
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#2: Protein | Mass: 69853.320 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 422-1005 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: SP3-BS71 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: A5LBQ0 | ||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9761 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9761 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 99648 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.9→38.46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.832 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.131 / 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: 16.205 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→38.46 Å
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Refine LS restraints |
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