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Yorodumi- PDB-7xac: Dimeric structure of human galectin-7 in complex with two glycerol -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xac | ||||||
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Title | Dimeric structure of human galectin-7 in complex with two glycerol | ||||||
Components | Galectin-7 | ||||||
Keywords | SUGAR BINDING PROTEIN / APOPTOSIS | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Si, Y.L. | ||||||
Funding support | China, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Binding of Glycerol to Human Galectin-7 Expands Stability and Modulates Its Functions. Authors: Liang, Y. / Wang, Y. / Zhu, X. / Cai, J. / Shi, A. / Huang, J. / Zhu, Q. / Si, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xac.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xac.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xac_validation.pdf.gz | 962.1 KB | Display | wwPDB validaton report |
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Full document | 7xac_full_validation.pdf.gz | 964 KB | Display | |
Data in XML | 7xac_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7xac_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/7xac ftp://data.pdbj.org/pub/pdb/validation_reports/xa/7xac | HTTPS FTP |
-Related structure data
Related structure data | 7xblC 1bkzS S: Starting model for refinement C: citing same article (ref.) |
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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: 15097.046 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli (E. coli) / References: UniProt: P47929 #2: Chemical | #3: 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: 2.05 Å3/Da / Density % sol: 40.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2M Magnesium chloride, 0.1M Hepes pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.85 Å / Num. obs: 23618 / % possible obs: 99.7 % / Redundancy: 1 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.001 / Num. unique obs: 1388 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BKZ Resolution: 1.8→19.85 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.7 / 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: 66.57 Å2 / Biso mean: 18.9185 Å2 / Biso min: 1.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→19.85 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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