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Yorodumi- PDB-2ya5: Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ya5 | ||||||
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Title | Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in complex with sialic acid | ||||||
Components | NEURAMINIDASE A | ||||||
Keywords | HYDROLASE / SIALIDASE | ||||||
Function / homology | Function and homology information ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gut, H. / Xu, G. / Taylor, G.L. / Walsh, M.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structural Basis for Streptococcus Pneumoniae Nana Inhibition by Influenza Antivirals Zanamivir and Oseltamivir Carboxylate. Authors: Gut, H. / Xu, G. / Taylor, G.L. / Walsh, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ya5.cif.gz | 209.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ya5.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ya5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/2ya5 ftp://data.pdbj.org/pub/pdb/validation_reports/ya/2ya5 | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8308, -0.4673, 0.3023), Vector: |
-Components
#1: Protein | Mass: 55346.684 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 280-754 Source method: isolated from a genetically manipulated source Details: THE SEQUENCE NUMBERING ABOVE CORRESPONDS TO THE CLOSEST UNIPROT SEQUENCE MATCH UNP B2DJD9. THE SEQUENCE NUMBERING FOR THE ENTRY SHOULD BE 303-777 Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: B2DJD9, UniProt: P62575*PLUS, exo-alpha-sialidase #2: Sugar | #3: Chemical | ChemComp-FMT / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | HYPOTHETICAL PROTEIN SPNET_02001817 STREPTOCOCCUS PNEUMONIAE TIGR4. APPARENT CONFLICTS ARE DUE TO ...HYPOTHETIC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % / Description: NONE |
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Crystal grow | Details: 20% PEG 3350, 200MM K FORMATE, 20MM TRIS PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 64851 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.8 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.213 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.197 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.134 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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