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Yorodumi- PDB-7a54: Two copies of the catalytic domain of NanA sialidase from Strepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a54 | ||||||
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Title | Two copies of the catalytic domain of NanA sialidase from Streptococcus pneumoniae juxtaposed in the P212121 space group, in complex with DANA | ||||||
Components | Sialidase A | ||||||
Keywords | STRUCTURAL PROTEIN / Sialidase / Catalytic domain / DANA | ||||||
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: 2.7 Å | ||||||
Authors | Bridot, C. / Bouckaert, J. | ||||||
Funding support | France, 1items
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Citation | Journal: Chemistry / Year: 2021 Title: Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases*. Authors: Assailly, C. / Bridot, C. / Saumonneau, A. / Lottin, P. / Roubinet, B. / Krammer, E.M. / Francois, F. / Vena, F. / Landemarre, L. / Alvarez Dorta, D. / Deniaud, D. / Grandjean, C. / Tellier, ...Authors: Assailly, C. / Bridot, C. / Saumonneau, A. / Lottin, P. / Roubinet, B. / Krammer, E.M. / Francois, F. / Vena, F. / Landemarre, L. / Alvarez Dorta, D. / Deniaud, D. / Grandjean, C. / Tellier, C. / Pascual, S. / Montembault, V. / Fontaine, L. / Daligault, F. / Bouckaert, J. / Gouin, S.G. #1: Journal: Chemistry / Year: 2019 Title: Multivalent Thiosialosides and Their Synergistic Interaction with Pathogenic Sialidases. Authors: Brissonnet, Y. / Assailly, C. / Saumonneau, A. / Bouckaert, J. / Maillasson, M. / Petitot, C. / Roubinet, B. / Didak, B. / Landemarre, L. / Bridot, C. / Blossey, R. / Deniaud, D. / Yan, X. / ...Authors: Brissonnet, Y. / Assailly, C. / Saumonneau, A. / Bouckaert, J. / Maillasson, M. / Petitot, C. / Roubinet, B. / Didak, B. / Landemarre, L. / Bridot, C. / Blossey, R. / Deniaud, D. / Yan, X. / Bernard, J. / Tellier, C. / Grandjean, C. / Daligault, F. / Gouin, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a54.cif.gz | 369.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a54.ent.gz | 296.8 KB | Display | PDB format |
PDBx/mmJSON format | 7a54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/7a54 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/7a54 | HTTPS FTP |
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-Related structure data
Related structure data | 7a5xC 2ya5S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
#1: Protein | Mass: 56141.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: nanA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62575, exo-alpha-sialidase #2: Sugar | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.45 Å3/Da / Density % sol: 49.81 % / Description: Beam |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 15% w/v Jeffamine ED 2003, 10% v/v ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→48.1 Å / Num. obs: 31218 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 68.757 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.205 / Net I/σ(I): 9.06 |
Reflection shell | Resolution: 2.28→2.42 Å / Redundancy: 11.14 % / Rmerge(I) obs: 0.3775 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 7560 / CC1/2: 0.384 / Rrim(I) all: 0.3954 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YA5 Resolution: 2.7→35.27 Å / SU ML: 0.3182 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2261 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.6 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→35.27 Å
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Refine LS restraints |
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LS refinement shell |
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