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Yorodumi- PDB-7z63: Structure of the LecA lectin from Pseudomonas aeruginosa in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z63 | ||||||
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Title | Structure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside | ||||||
Components | PA-I galactophilic lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / antiadhesive / thiogalactoside / RNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Varrot, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: Discovery of potent 1,1-diarylthiogalactoside glycomimetic inhibitors of Pseudomonas aeruginosa LecA with antibiofilm properties. Authors: Bruneau, A. / Gillon, E. / Furiga, A. / Brachet, E. / Alami, M. / Roques, C. / Varrot, A. / Imberty, A. / Messaoudi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z63.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z63.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z63_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7z63_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7z63_validation.xml.gz | 31 KB | Display | |
Data in CIF | 7z63_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/7z63 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z63 | HTTPS FTP |
-Related structure data
Related structure data | 7z62C 1okoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12770.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N terminal methionine cleaved / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lecA, pa1L, PA2570 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05097 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-IE3 / [ #4: Chemical | ChemComp-EDO / | #5: 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: 2.31 Å3/Da / Density % sol: 46.87 % / Description: rod |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: LecA was dissolved in 20 mM Tris HCl pH 8.0 and 100 mM NaCl to a concentration of 16.9 mgmL and incubated for 3h at room temperature with 3.8 mM of compound. drops were made using the ...Details: LecA was dissolved in 20 mM Tris HCl pH 8.0 and 100 mM NaCl to a concentration of 16.9 mgmL and incubated for 3h at room temperature with 3.8 mM of compound. drops were made using the supernatant after centrifugation at 20000 g for 5 minutes since precipitation was observed and a crystallization solution containing 18% PEG3350, 150 mM potassium thiocyanate (KSCN) and 100 mM Tris HCl pH 8.5 |
-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: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45 Å / Num. obs: 48775 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2627 / CC1/2: 0.976 / Rpim(I) all: 0.186 / Rrim(I) all: 0.347 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OKO Resolution: 1.75→43.131 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.267 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.117 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.085 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→43.131 Å
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Refine LS restraints |
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LS refinement shell |
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