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Yorodumi- PDB-7n8d: Crystal structure of R22A human Galectin-7 mutant in presence of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n8d | |||||||||||||||||||||
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Title | Crystal structure of R22A human Galectin-7 mutant in presence of Lactose | |||||||||||||||||||||
Components | (Galectin-7) x 2 | |||||||||||||||||||||
Keywords | SUGAR BINDING PROTEIN / human galectin-7 / dimer interface mutant / lactose | |||||||||||||||||||||
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: 2.49 Å | |||||||||||||||||||||
Authors | Pham, N.T.H. / Calmettes, C. / Doucet, N. | |||||||||||||||||||||
Funding support | Canada, United States, 6items
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Citation | Journal: To Be Published Title: Crystal structure of R22A human Galectin-7 mutant in presence of Lactose Authors: Pham, N.T.H. / 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 | 7n8d.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n8d.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 7n8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n8d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7n8d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7n8d_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 7n8d_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n8d ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n8d | HTTPS FTP |
-Related structure data
Related structure data | 4galS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14879.734 Da / Num. of mol.: 1 / Mutation: R22A 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 | ||||||
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#2: Protein | Mass: 14895.734 Da / Num. of mol.: 1 / Mutation: R22A 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 | ||||||
#3: Polysaccharide | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: 44.78 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 7.5 mM alpha Lactose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 19, 2019 / Details: 16 tiled fiber-optic tapers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→45.4 Å / Num. obs: 9873 / % possible obs: 99.6 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.025 / Rrim(I) all: 0.073 / Net I/σ(I): 22.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.49→31.89 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.35 / 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: 59.21 Å2 / Biso mean: 27.3596 Å2 / Biso min: 12.06 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.49→31.89 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: 4
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