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- PDB-4ce8: Perdeuterated Pseudomonas aeruginosa Lectin II complex with hydro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ce8 | |||||||||
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Title | Perdeuterated Pseudomonas aeruginosa Lectin II complex with hydrogenated L-Fucose and Calcium | |||||||||
![]() | FUCOSE-BINDING LECTIN PA-IIL | |||||||||
![]() | SUGAR BINDING PROTEIN / PERDEUTERATED | |||||||||
Function / homology | ![]() single-species biofilm formation / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cuypers, M.G. / Mitchell, E.P. / Mossou, E. / Pokorna, M. / Wimmerova, M. / Imberty, A. / Moulin, M. / Haertlein, M. / Forsyth, V.T. | |||||||||
![]() | ![]() Title: Perdeuterated Pseudomonas Aeruginosa Lectin II Complex with Hydrogenated L Fucose and Calcium Authors: Cuypers, M.G. / Mossou, E. / Mitchell, E.P. / Russi, S. / Pokorna, M. / Wimmerova, M. / Imberty, A. / Mcsweeney, S. / Haertlein, M. / Forsyth, V.T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.9 KB | Display | ![]() |
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PDB format | ![]() | 252.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.1 KB | Display | ![]() |
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Full document | ![]() | 482.7 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uzvS S: Starting model for refinement |
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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
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/FUC.gif)
![](data/chem/img/FUC.gif)
#1: Protein | Mass: 11734.707 Da / Num. of mol.: 4 / Fragment: 2-115 Source method: isolated from a genetically manipulated source Details: PERDEUTERATED PROTEIN / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Sugar | ChemComp-FUC / |
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-Non-polymers , 4 types, 1007 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-URE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % Description: NEEDED ONLY 2 CA ATOMS FROM 1UZV FOR ISOMORPHOUS REPLACEMENT WITH ACORN. |
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Crystal grow | Method: vapor diffusion, hanging drop Details: ALL SALTS EXCHANGED 3X AGAINST D2O. 0,1 M TRIS PD 8.5, 1.75M (ND4)2SO4, 2MM CACL2, 2MM MGCL2. 10 MG/ML PROTEIN PRE-INCUBATED IN 2MM CACL2 AND 250 MG/L L-FUCOSE. HANGING DROP METHOD. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→43.55 Å / Num. obs: 291511 / % possible obs: 97.1 % / Observed criterion σ(I): 1.8 / Redundancy: 3 % / Biso Wilson estimate: 6.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2 |
Reflection shell | Highest resolution: 0.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UZV Resolution: 0.9→36.463 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 13.29 / Stereochemistry target values: ML Details: UREA FOUND NEARBY ARGININES, PARTIAL DEGRADATION POSSIBLE INTO ORNITHINE.
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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 mean: 4.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→36.463 Å
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Refine LS restraints |
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LS refinement shell |
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