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Yorodumi- PDB-4a6s: Structure of the PAIL lectin from Pseudomonas aeruginosa in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a6s | ||||||
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Title | Structure of the PAIL lectin from Pseudomonas aeruginosa in complex with 2-Naphtyl-1-thio-beta-D-galactopyranoside | ||||||
Components | PA-I GALACTOPHILIC LECTIN | ||||||
Keywords | SUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / GLYCOMIMETIC | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Rodrigue, J. / Ganne, G. / Blanchard, B. / Saucier, C. / Giguere, D. / Chiao, T.S. / Varrot, A. / Imberty, A. / Roy, R. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2013 Title: Aromatic Thioglycoside Inhibitors Against the Virulence Factor Leca from Pseudomonas Aeruginosa. Authors: Rodrigue, J. / Ganne, G. / Blanchard, B. / Saucier, C. / Giguere, D. / Shiao, T.C. / Varrot, A. / Imberty, A. / Roy, R. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a6s.cif.gz | 199.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a6s.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6s ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6s | HTTPS FTP |
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-Related structure data
Related structure data | 1okoS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 12770.137 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097 #2: Chemical | ChemComp-CA / #3: Sugar | ChemComp-GS9 / #4: Water | ChemComp-HOH / | Sequence details | ALL NUMBERING SHIFTED BY 1 SINCE N-TERMINAL METHIONINE | |
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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: 3.06 Å3/Da / Density % sol: 59.78 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 0.8 M LISO4, 100 MM SODIUM ACETATE PH 4.5, 25% GLYCEROL (ADDED FOR CRYPROTECTION). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97623 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 37963 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OKO Resolution: 2.15→38.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.076 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.188 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.949 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→38.13 Å
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Refine LS restraints |
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