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- PDB-6rgg: Photorhabdus laumondii lectin PLL2 in complex with O-methylated P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rgg | ||||||
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Title | Photorhabdus laumondii lectin PLL2 in complex with O-methylated PGL-1-derived disaccharide | ||||||
![]() | lectin PLL2 from Photorhabdus laumondii | ||||||
![]() | SUGAR BINDING PROTEIN / lectin / Photorhabdus / PGL-1 / O-methylated saccharide / beta-propeller | ||||||
Function / homology | Protein of unknown function DUF346 / Repeat of unknown function (DUF346) / 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose / 3,6-O-dimethyl-D-glucose / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Houser, J. / Fujdiarova, E. / Wimmerova, M. | ||||||
![]() | ![]() Title: Heptabladed beta-propeller lectins PLL2 and PHL from Photorhabdus spp. recognize O-methylated sugars and influence the host immune system. Authors: Fujdiarova, E. / Houser, J. / Dobes, P. / Paulikova, G. / Kondakov, N. / Kononov, L. / Hyrsl, P. / Wimmerova, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.1 KB | Display | ![]() |
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PDB format | ![]() | 112.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.4 KB | Display | ![]() |
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Full document | ![]() | 489 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rfzC ![]() 6rg1C ![]() 6rg2C ![]() 6rgjC ![]() 6rgrC ![]() 6rguC ![]() 6rgwC 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
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/7CV.gif)
![](data/chem/img/7CV.gif)
#1: Protein | Mass: 40150.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: plu0734 / Plasmid: pET25-b / Production host: ![]() ![]() #3: Sugar | |
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-Non-polymers , 4 types, 28 molecules ![](data/chem/img/K3Q.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-K3Q / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 12.5% PEG 4000, 0.1 M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→67.03 Å / Num. obs: 40910 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 46.387 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5878 / CC1/2: 0.541 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.054 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→67.03 Å
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Refine LS restraints |
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