+Open data
-Basic information
Entry | Database: PDB / ID: 5nlz | ||||||
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Title | GRIFIN (Crystallisation pH: 4.2) | ||||||
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: 1.149 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 | 5nlz.cif.gz | 180.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nlz.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nlz_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 5nlz_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 5nlz_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5nlz_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/5nlz ftp://data.pdbj.org/pub/pdb/validation_reports/nl/5nlz | HTTPS FTP |
-Related structure data
Related structure data | 5nldSC 5nleC 5nlhC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16205.410 Da / Num. of mol.: 2 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: 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: 1.98 Å3/Da / Density % sol: 37.85 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: Crystallization condition 20% PEG 8K, 0.1M phosphate-citrate pH 4.2, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.149 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.149 Å / Relative weight: 1 |
Reflection | Resolution: 1.149→39.054 Å / Num. obs: 85844 / % possible obs: 95.61 % / Redundancy: 1.6 % / Biso Wilson estimate: 10.26 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.024 / Net I/σ(I): 12.53 |
Reflection shell | Resolution: 1.149→1.19 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 7759 / CC1/2: 0.82 / % possible all: 86.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NLD Resolution: 1.149→39.054 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.149→39.054 Å
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Refine LS restraints |
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LS refinement shell |
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