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Yorodumi- PDB-2vw2: Crystal structure of the NanB sialidase from Streptococcus pneumoniae -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vw2 | ||||||
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Title | Crystal structure of the NanB sialidase from Streptococcus pneumoniae | ||||||
Components | SIALIDASE B | ||||||
Keywords | HYDROLASE / SIALIDASE / GLYCOSIDASE / DRUG DESIGN / NEURAMINIDASE / VIRULENCE FACTOR | ||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Xu, G. / Potter, J.A. / Russell, R.J.M. / Oggioni, M.R. / Andrew, P.W. / Taylor, G.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal Structure of the Nanb Sialidase from Streptococcus Pneumoniae Authors: Xu, G. / Potter, J.A. / Russell, R.J.M. / Oggioni, M.R. / Andrew, P.W. / Taylor, G.L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vw2.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vw2.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vw2 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vw2 | HTTPS FTP |
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-Related structure data
Related structure data | 2vw0C 2vw1C 1sliS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 77780.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54727, exo-alpha-sialidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.51 % / Description: NONE |
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Crystal grow | pH: 9.5 / Details: 10% PEG 8000, 0.15M NACL, 0.1M CHES PH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 75667 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.2 / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SLI Resolution: 1.7→67.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.719 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.118 / 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: 18.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→67.42 Å
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Refine LS restraints |
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