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Yorodumi- PDB-5a3o: Crystal structure of the LecB lectin from Pseudomonas aeruginosa ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a3o | ||||||
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Title | Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(cinnamido)-6-deoxy-alpha-D-mannopyranoside at 1.6 ansgtrom | ||||||
Components | FUCOSE-BINDING LECTIN PA-IIL | ||||||
Keywords | SUGAR BINDING PROTEIN / GLYCOINHIBITORS | ||||||
Function / homology | Function and homology information single-species biofilm formation / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sommer, R. / Hauck, D. / Varrot, A. / Audfray, A. / Imberty, A. / Titz, A. | ||||||
Citation | Journal: Chemistryopen / Year: 2015 Title: Cinnamide Derivatives of D-Mannose as Inhibitors of the Bacterial Virulence Factor Lecb from Pseudomonas Aeruginosa Authors: Sommer, R. / Hauck, D. / Varrot, A. / Wagner, S. / Audfray, A. / Prestel, A. / Moleer, H.M. / Imberty, A. / Titz, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a3o.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a3o.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a3o_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
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Full document | 5a3o_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 5a3o_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 5a3o_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a3o ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a3o | HTTPS FTP |
-Related structure data
Related structure data | 3zdvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114
NCS ensembles :
NCS oper:
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 11734.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N TERMINAL METHIONINE CLEAVED / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25PA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5 #3: Sugar | ChemComp-MMA / |
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-Non-polymers , 4 types, 637 molecules
#2: Chemical | ChemComp-CA / #4: Chemical | ChemComp-DH6 / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | 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: 2.17 Å3/Da / Density % sol: 43.3 % / Description: NONE |
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Crystal grow | pH: 3.8 Details: 25% PEG 6K, 100MM CITRIC ACID PH 3.8 AND 1L LITHIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→1.85 Å / Num. obs: 50076 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.1 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZDV Resolution: 1.6→39.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.803 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 8.769 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→39.25 Å
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Refine LS restraints |
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