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- PDB-2vxj: CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vxj | |||||||||
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Title | CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC AT 1.9 A RESOLUTION | |||||||||
![]() | PA-I GALACTOPHILIC LECTIN | |||||||||
![]() | SUGAR BINDING PROTEIN / LECTIN / GLOBOSIDE | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Blanchard, B. / Nurisso, A. / Hollville, E. / Tetaud, C. / Wiels, J. / Pokorna, M. / Wimmerova, M. / Varrot, A. / Imberty, A. | |||||||||
![]() | ![]() Title: Structural Basis of the Preferential Binding for Globo-Series Glycosphingolipids Displayed by Pseudomonas Aeruginosa Lectin I. Authors: Blanchard, B. / Nurisso, A. / Hollville, E. / Tetaud, C. / Wiels, J. / Pokorna, M. / Wimmerova, M. / Varrot, A. / Imberty, A. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 619 KB | Display | ![]() |
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PDB format | ![]() | 514.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.5 MB | Display | ![]() |
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Full document | ![]() | 7.6 MB | Display | |
Data in XML | ![]() | 138.1 KB | Display | |
Data in CIF | ![]() | 196.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1l7lS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
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Components
-Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX
#1: Protein | Mass: 12770.137 Da / Num. of mol.: 24 / Fragment: RESIDUES 2-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 4 types, 25 molecules ![](data/chem/img/BGC.gif)
#2: Polysaccharide | alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-BGC / | |
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-Non-polymers , 3 types, 3090 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINAL METHIONINE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 10% PEG 5000 MME, 0.025M KSCN, 0.1M NAAC PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 30, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→55.22 Å / Num. obs: 230909 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.26 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.45 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.08 / % possible all: 89.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L7L Resolution: 1.9→55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.886 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.165 / 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: 10.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→55 Å
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Refine LS restraints |
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