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Yorodumi- PDB-6flu: Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6flu | ||||||
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Title | Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside | ||||||
Components | Photorhabdus asymbitoca lectin PHL | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / seven-bladed beta-propeller / C-fucoside / Methyl 2 / 3-dideoxy-3-C-[(a-L-fucopyranosyl)methyl]-a-D- arabino-hexopyranoside | ||||||
Function / homology | Repeat of unknown function (DUF346) / metal ion binding / Chem-DTK / Bulb-type lectin domain-containing protein Function and homology information | ||||||
Biological species | Photorhabdus asymbiotica subsp. asymbiotica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Houser, J. / Jancarikova, G. / Wimmerova, M. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Fucosylated inhibitors of recently identified bangle lectin from Photorhabdus asymbiotica. Authors: Paulikova, G. / Houser, J. / Kasakova, M. / Oroszova, B. / Bertolotti, B. / Parkan, K. / Moravcova, J. / Wimmerova, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6flu.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6flu.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 6flu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/6flu ftp://data.pdbj.org/pub/pdb/validation_reports/fl/6flu | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 40213.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria) Strain: ATCC 43949 / 3105-77 / Gene: PAU_00698 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner / References: UniProt: C7BLE4 #2: Chemical | ChemComp-DTK / ( #3: Chemical | #4: Chemical | ChemComp-CL / #5: 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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.7 M NaCl, 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8943 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→44.93 Å / Num. obs: 85234 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.991 / Rmerge(I) obs: 0.242 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.78→1.87 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.325 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 132122 / CC1/2: 0.53 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→44.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.969 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.112 / 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: 12.354 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→44.93 Å
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Refine LS restraints |
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