+Open data
-Basic information
Entry | Database: PDB / ID: 5jp5 | ||||||
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Title | Crystal structure of rat Galectin 5 | ||||||
Components | Galectin-5 | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin carbohydrate recognition jellyroll topology | ||||||
Function / homology | Function and homology information lactose binding / galactoside binding / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of T cell apoptotic process / negative regulation of type II interferon production / carbohydrate binding / positive regulation of gene expression / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ruiz, F.M. / Romero, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Biomolecules / Year: 2021 Title: Structural Characterization of Rat Galectin-5, an N-Tailed Monomeric Proto-Type-like Galectin. Authors: Ruiz, F.M. / Medrano, F.J. / Ludwig, A.K. / Kaltner, H. / Shilova, N.V. / Bovin, N.V. / Gabius, H.J. / Romero, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jp5.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jp5.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jp5_validation.pdf.gz | 480.2 KB | Display | wwPDB validaton report |
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Full document | 5jp5_full_validation.pdf.gz | 488 KB | Display | |
Data in XML | 5jp5_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 5jp5_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/5jp5 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/5jp5 | HTTPS FTP |
-Related structure data
Related structure data | 5jpgC 7p8hC 3nv1S 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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Unit cell |
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-Components
#1: Protein | Mass: 16212.335 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lgals5 / Production host: Escherichia coli (E. coli) / References: UniProt: P47967 #2: Chemical | ChemComp-PEG / #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: 2.23 Å3/Da / Density % sol: 44.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 8000, 100 mM Tris pH 7.0, 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: May 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.03 Å / Num. obs: 92950 / % possible obs: 99.75 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.01 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / % possible all: 99.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NV1 Resolution: 1.7→33.027 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→33.027 Å
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Refine LS restraints |
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LS refinement shell |
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