+Open data
-Basic information
Entry | Database: PDB / ID: 6n3r | ||||||
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Title | Sheep Galectin-11 (LGALS11) complex with galactose | ||||||
Components | Galectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Glycan binding / Galectin / Lectin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.397 Å | ||||||
Authors | Beddoe, T.C. / Sakthivel, D. | ||||||
Citation | Journal: To be Published Title: Sheep Galectin-11 (LGALS11) complex with galactose Authors: Beddoe, T.C. / Sakthivel, D. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Cloning, expression, purification and crystallographic studies of galectin-11 from domestic sheep (Ovis aries). Authors: Sakthivel, D. / Littler, D. / Shahine, A. / Troy, S. / Johnson, M. / Rossjohn, J. / Piedrafita, D. / Beddoe, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n3r.cif.gz | 243.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n3r.ent.gz | 195.3 KB | Display | PDB format |
PDBx/mmJSON format | 6n3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n3r_validation.pdf.gz | 500 KB | Display | wwPDB validaton report |
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Full document | 6n3r_full_validation.pdf.gz | 507.4 KB | Display | |
Data in XML | 6n3r_validation.xml.gz | 51.2 KB | Display | |
Data in CIF | 6n3r_validation.cif.gz | 74.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/6n3r ftp://data.pdbj.org/pub/pdb/validation_reports/n3/6n3r | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15580.910 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Strain: Merino / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A7EMW6 #2: Sugar | ChemComp-GAL / #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: 3.45 Å3/Da / Density % sol: 64.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% v/v Tacsimate, pH 7.0, 0.1 M HEPES, pH 7.5, 20% w/v PEG3350 PH range: 7.3 - 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 6, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.397→47.169 Å / Num. obs: 68286 / % possible obs: 99.97 % / Redundancy: 7.9 % / Biso Wilson estimate: 22.3 Å2 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.71→2.81 Å |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.397→47.169 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.18 Å2 / Biso mean: 24.3736 Å2 / Biso min: 7.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.397→47.169 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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