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Yorodumi- PDB-7a5x: Two copies of the catalytic domain of NanA sialidase from Strepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a5x | ||||||
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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 derivatized with a PEG linker on the glycerol group. | ||||||
Components | Sialidase A | ||||||
Keywords | STRUCTURAL PROTEIN / Sialidase / Catalytic domain / CA170 | ||||||
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 / extracellular region Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a5x.cif.gz | 382.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a5x.ent.gz | 307.3 KB | Display | PDB format |
PDBx/mmJSON format | 7a5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/7a5x ftp://data.pdbj.org/pub/pdb/validation_reports/a5/7a5x | HTTPS FTP |
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-Related structure data
Related structure data | 7a54C 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 756 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.4 Å3/Da / Density % sol: 48.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Ammonium sulfate, 0.1M Tris pH=8,5 35% w/v PEG 3350 |
-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: Jan 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→56.6 Å / Num. obs: 80186 / % possible obs: 99.3 % / Redundancy: 8.43 % / Biso Wilson estimate: 38.564 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.171 / Net I/σ(I): 10.02 |
Reflection shell | Resolution: 1.94→2.06 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.1628 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 12318 / CC1/2: 0.477 / Rrim(I) all: 0.1731 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YA5 Resolution: 1.94→56.6 Å / SU ML: 0.2973 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0805 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: 46.6 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→56.6 Å
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Refine LS restraints |
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LS refinement shell |
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