+Open data
-Basic information
Entry | Database: PDB / ID: 6rgj | ||||||
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Title | Photorhabdus asymbiotica lectin PHL in complex with D-glucose | ||||||
Components | Lectin PHL | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / Photorhabdus / glucose / beta-propeller | ||||||
Function / homology | Repeat of unknown function (DUF346) / metal ion binding / beta-D-glucopyranose / Bulb-type lectin domain-containing protein Function and homology information | ||||||
Biological species | Photorhabdus asymbiotica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Houser, J. / Fujdiarova, E. / Jancarikova, G. / Wimmerova, M. | ||||||
Citation | Journal: Febs J. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rgj.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rgj.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/6rgj ftp://data.pdbj.org/pub/pdb/validation_reports/rg/6rgj | HTTPS FTP |
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-Related structure data
Related structure data | 6rfzC 6rg1C 6rg2C 6rggC 6rgrC 6rguC 6rgwC 5mxeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
-Protein / Sugars , 2 types, 5 molecules A
#1: Protein | Mass: 40213.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus asymbiotica (bacteria) / Gene: PAU_00698 / Plasmid: pET25-b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner / References: UniProt: C7BLE4 |
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#3: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 369 molecules
#2: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.9 M NaCl, 100 mM Hepes, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.895 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.03 Å / Num. obs: 40112 / % possible obs: 99.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 10.799 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 5670 / CC1/2: 0.895 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MXE Resolution: 1.8→44.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.38 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / 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: 15.492 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.03 Å
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Refine LS restraints |
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