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Yorodumi- PDB-6vtq: Crystal structure of G16C human Galectin-7 mutant in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vtq | |||||||||||||||||||||
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Title | Crystal structure of G16C human Galectin-7 mutant in complex with lactose | |||||||||||||||||||||
Components | Galectin-7 | |||||||||||||||||||||
Keywords | SUGAR BINDING PROTEIN / Human Galectin-7 / lactose / G16C mutant / disulfide bond | |||||||||||||||||||||
Function / homology | Function and homology information heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | |||||||||||||||||||||
Authors | Pham, N.T.H. / Calmettes, C. / Doucet, N. | |||||||||||||||||||||
Funding support | Canada, United States, 6items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7. Authors: Pham, N.T.H. / Letourneau, M. / Fortier, M. / Begin, G. / Al-Abdul-Wahid, M.S. / Pucci, F. / Folch, B. / Rooman, M. / Chatenet, D. / St-Pierre, Y. / Lague, P. / Calmettes, C. / Doucet, N. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vtq.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vtq.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vtq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vtq_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6vtq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6vtq_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6vtq_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/6vtq ftp://data.pdbj.org/pub/pdb/validation_reports/vt/6vtq | HTTPS FTP |
-Related structure data
Related structure data | 6vtoC 6vtpC 6vtrC 6vtsC 4galS 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: 15027.941 Da / Num. of mol.: 2 / Mutation: G16C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47929 #2: Polysaccharide | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.87 Å3/Da / Density % sol: 34.15 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris pH 8, 0.1 M Sodium Chloride, 25 % PEG3350, 7.5 mM alpha-lactose Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ACCEL/BRUKER double crystal mocochromator (DCM,Si-111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→42.66 Å / Num. obs: 17138 / % possible obs: 100 % / Redundancy: 12.59 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.112 / Net I/σ(I): 16.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4gal Resolution: 1.95→42.66 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.06 / 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: 132.73 Å2 / Biso mean: 36.6079 Å2 / Biso min: 11.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→42.66 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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