+Open data
-Basic information
Entry | Database: PDB / ID: 5nle | |||||||||
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Title | Chicken GRIFIN (crystallisation pH: 8.0) | |||||||||
Components | Galectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / Galectin related protein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 Å | |||||||||
Authors | Ruiz, F.M. / Romero, A. | |||||||||
Funding support | 1items
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Citation | Journal: Biochimie / Year: 2018 Title: Chicken GRIFIN: Structural characterization in crystals and in solution. Authors: Ruiz, F.M. / Gilles, U. / Ludwig, A.K. / Sehad, C. / Shiao, T.C. / Garcia Caballero, G. / Kaltner, H. / Lindner, I. / Roy, R. / Reusch, D. / Romero, A. / Gabius, H.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nle.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nle.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 5nle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/5nle ftp://data.pdbj.org/pub/pdb/validation_reports/nl/5nle | HTTPS FTP |
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-Related structure data
Related structure data | 5nldSC 5nlhC 5nlzC 5nm1C 5nm6C 5nmjC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16205.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: GRIFIN / Production host: Escherichia coli (E. coli) / References: UniProt: F1NZ18 #2: Polysaccharide | beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose #3: 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: 2.39 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 10% PEG 3K, 0.1M Imidazole pH 8.0, 0.2M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→35.21 Å / Num. obs: 54344 / % possible obs: 99.75 % / Redundancy: 2 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 14.12 |
Reflection shell | Resolution: 1.84→1.91 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 5238 / CC1/2: 0.63 / % possible all: 97.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NLD Resolution: 1.845→35.21 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.845→35.21 Å
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Refine LS restraints |
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LS refinement shell |
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