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Yorodumi- PDB-6rgw: Photorhabdus asymbiotica lectin PHL in complex with O-methylated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rgw | ||||||
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Title | Photorhabdus asymbiotica lectin PHL in complex with O-methylated PGL-1-derived disaccharide | ||||||
Components | Lectin PHL | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / Photorhabdus / O-methylated saccharide / PGL-1 / beta-propeller | ||||||
Function / homology | Repeat of unknown function (DUF346) / metal ion binding / 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose / 3,6-O-dimethyl-D-glucose / 4-(2-azanylethoxy)phenol / Bulb-type lectin domain-containing protein Function and homology information | ||||||
Biological species | Photorhabdus asymbiotica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 6rgw.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rgw.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rgw_validation.pdf.gz | 485.7 KB | Display | wwPDB validaton report |
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Full document | 6rgw_full_validation.pdf.gz | 486.6 KB | Display | |
Data in XML | 6rgw_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 6rgw_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/6rgw ftp://data.pdbj.org/pub/pdb/validation_reports/rg/6rgw | HTTPS FTP |
-Related structure data
Related structure data | 6rfzC 6rg1C 6rg2C 6rggC 6rgjC 6rgrC 6rguC 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, 3 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(DE3) / References: UniProt: C7BLE4 |
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#3: Sugar |
-Non-polymers , 6 types, 276 molecules
#2: Chemical | ChemComp-K3Q / #4: Chemical | ChemComp-K42 / | #5: Chemical | ChemComp-EDO / | #6: Chemical | #7: Chemical | ChemComp-CL / | #8: 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: 2.86 Å3/Da / Density % sol: 57.04 % |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
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→44.13 Å / Num. obs: 44002 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 28.891 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6338 / CC1/2: 0.723 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MXE Resolution: 1.75→40.48 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.505 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.101 / 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: 29.377 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40.48 Å
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Refine LS restraints |
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