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Yorodumi- PDB-5c9o: Crystal structure of recombinant PLL lectin from Photorhabdus lum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c9o | ||||||||||||
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Title | Crystal structure of recombinant PLL lectin from Photorhabdus luminescens at 1.5 A resolution | ||||||||||||
Components | PLL lectin | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Lectin / seven-bladed beta-propeller / fucose-specific | ||||||||||||
Function / homology | Protein of unknown function DUF346 / Repeat of unknown function (DUF346) / metal ion binding / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17 Function and homology information | ||||||||||||
Biological species | Photorhabdus luminescens (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Kumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / Hyrsl, P. / Wimmerova, M. | ||||||||||||
Funding support | Czech Republic, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure. Authors: Kumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / 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 | 5c9o.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c9o.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 5c9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c9o_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 5c9o_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | 5c9o_validation.xml.gz | 20 KB | Display | |
Data in CIF | 5c9o_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/5c9o ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c9o | HTTPS FTP |
-Related structure data
Related structure data | 5c9lSC 5c9pC 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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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) | |||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41944.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu0732 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N8J0 | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density meas: 998259.938 Mg/m3 / Density % sol: 57.78 % / Description: prism |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 2.5 % ethanol, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→79.17 Å / Num. obs: 80153 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 6.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C9L Resolution: 1.5→39.17 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.695 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.465 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→39.17 Å
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Refine LS restraints |
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