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Yorodumi- PDB-8jae: Crystal structure of E33A mutant human galectin-10 produced by ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jae | ||||||
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Title | Crystal structure of E33A mutant human galectin-10 produced by cell-free protein synthesis in complex with melezitose | ||||||
Components | Galectin-10CLC (gene) | ||||||
Keywords | SUGAR BINDING PROTEIN / Galectin / CLC | ||||||
Function / homology | Function and homology information regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate binding / collagen-containing extracellular matrix / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Kojima, M. / Ueno, T. / Abe, S. / Hirata, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Cell-free protein crystallization for rapid structure determination of multiple substrates Authors: Kojima, M. / Abe, S. / Hirata, K. / Ueno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jae.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jae.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 8jae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/8jae ftp://data.pdbj.org/pub/pdb/validation_reports/ja/8jae | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16413.797 Da / Num. of mol.: 1 / Mutation: E33A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free synthesis / Gene: CLC, LGALS10, LGALS10A / Production host: Triticum aestivum (bread wheat) / References: UniProt: Q05315 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-2)-[alpha-D-glucopyranose-(1-3)]beta-D-fructofuranose Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: 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: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / Details: cell-free crystallization |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 25346 / % possible obs: 99.8 % / Redundancy: 14.47 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.988 / Net I/σ(I): 10.52 |
Reflection shell | Resolution: 1.62→1.72 Å / Num. unique obs: 4028 / CC1/2: 0.704 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→42.57 Å / SU ML: 0.196 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6903 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 17.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→42.57 Å
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Refine LS restraints |
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LS refinement shell |
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