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Yorodumi- PDB-6rg2: Photorhabdus laumondii lectin PLL2 in complex with 3-O-methyl-D-g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rg2 | ||||||
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Title | Photorhabdus laumondii lectin PLL2 in complex with 3-O-methyl-D-glucose | ||||||
Components | lectin PLL2 from Photorhabdus laumondii | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / Photorhabdus / 3-O-methyl-D-glucose / 3OMG / beta-propeller | ||||||
Function / homology | Protein of unknown function DUF346 / Repeat of unknown function (DUF346) / 3-O-methyl-beta-D-glucopyranose / ACETATE ION / 3-O-methyl-alpha-D-glucopyranose / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17 Function and homology information | ||||||
Biological species | Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Houser, J. / Fujdiarova, E. / 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 | 6rg2.cif.gz | 338.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rg2.ent.gz | 273 KB | Display | PDB format |
PDBx/mmJSON format | 6rg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rg2_validation.pdf.gz | 484.7 KB | Display | wwPDB validaton report |
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Full document | 6rg2_full_validation.pdf.gz | 489.9 KB | Display | |
Data in XML | 6rg2_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 6rg2_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/6rg2 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/6rg2 | HTTPS FTP |
-Related structure data
Related structure data | 6rfzC 6rg1C 6rggC 6rgjC 6rgrC 6rguC 6rgwC 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
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 40150.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) Gene: plu0734 / Plasmid: pET25-b / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q7N8I8 |
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-Sugars , 2 types, 19 molecules
#2: Sugar | ChemComp-ZB1 / #3: Sugar | ChemComp-3MG / |
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-Non-polymers , 3 types, 1066 molecules
#4: Chemical | ChemComp-ACT / #5: Chemical | #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: 1.97 Å3/Da / Density % sol: 37.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 11% PEG 4000, 150 mM sodium acetate pH 4.6 |
-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: 1.12→44.84 Å / Num. obs: 224157 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 7.939 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.12→1.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 16606 / CC1/2: 0.74 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→44.84 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.574 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / 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: 12.321 Å2
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Refinement step | Cycle: 1 / Resolution: 1.12→44.84 Å
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Refine LS restraints |
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