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- PDB-4yw6: Structural Insight into Divalent Galactoside Binding to Pseudomon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yw6 | ||||||
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Title | Structural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA | ||||||
![]() | PA-I galactophilic lectin | ||||||
![]() | SUGAR BINDING PROTEIN / Galactosides / lectins | ||||||
Function / homology | ![]() heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Visini, R. / Jin, X. / Michaud, G. / Bergmann, M. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. / Pieters, R. / Reymond, J.-L. | ||||||
![]() | ![]() Title: Structural Insight into Multivalent Galactoside Binding to Pseudomonas aeruginosa Lectin LecA. Authors: Visini, R. / Jin, X. / Bergmann, M. / Michaud, G. / Pertici, F. / Fu, O. / Pukin, A. / Branson, T.R. / Thies-Weesie, D.M. / Kemmink, J. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. ...Authors: Visini, R. / Jin, X. / Bergmann, M. / Michaud, G. / Pertici, F. / Fu, O. / Pukin, A. / Branson, T.R. / Thies-Weesie, D.M. / Kemmink, J. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. / Pieters, R.J. / Reymond, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.5 KB | Display | ![]() |
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PDB format | ![]() | 101.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 46.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yw7C ![]() 4ywaC ![]() 1okoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-G0P / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.5M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→67.032 Å / Num. all: 129508 / Num. obs: 129508 / % possible obs: 84.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.45 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.071 / Rsym value: 0.058 / Net I/av σ(I): 4.983 / Net I/σ(I): 7.7 / Num. measured all: 380562 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1oko Resolution: 1.4→23.934 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.37 Å2 / Biso mean: 18.9842 Å2 / Biso min: 4.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→23.934 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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