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- PDB-6rgu: Photorhabdus asymbiotica lectin PHL in complex with 3-O-methyl-D-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rgu | ||||||
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Title | Photorhabdus asymbiotica lectin PHL in complex with 3-O-methyl-D-glucose | ||||||
![]() | Lectin PHL | ||||||
![]() | SUGAR BINDING PROTEIN / lectin / Photorhabdus / 3-O-methyl-d-glucose / 3OMG / beta-propeller | ||||||
Function / homology | Repeat of unknown function (DUF346) / metal ion binding / 3-O-methyl-beta-D-glucopyranose / Bulb-type lectin domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Houser, J. / Fujdiarova, E. / Jancarikova, G. / 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 | ![]() | 91.6 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.5 KB | Display | ![]() |
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Full document | ![]() | 452.7 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rfzC ![]() 6rg1C ![]() 6rg2C ![]() 6rggC ![]() 6rgjC ![]() 6rgrC ![]() 6rgwC ![]() 5mxeS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 40213.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Sugar | ChemComp-3MG / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4M NaCl, 100mM Hepes, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→44.02 Å / Num. obs: 43779 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 26.515 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6310 / CC1/2: 0.693 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MXE Resolution: 1.75→40.45 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.386 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.942 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40.45 Å
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Refine LS restraints |
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