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Yorodumi- PDB-3w59: Crystal structure of Galectin-1 in the lactose-unbound state(P212121) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w59 | ||||||
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Title | Crystal structure of Galectin-1 in the lactose-unbound state(P212121) | ||||||
Components | Galectin-1 | ||||||
Keywords | SUGAR BINDING PROTEIN / lactose unbound state / Galectin / lectin | ||||||
Function / homology | Function and homology information galectin complex / lactose binding / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...galectin complex / lactose binding / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Saburi, H. / Tanaka, T. / Kunishima, N. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Galectin-1 in the lactose-unbound state Authors: Saburi, H. / Tanaka, T. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w59.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w59.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w59_validation.pdf.gz | 479.7 KB | Display | wwPDB validaton report |
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Full document | 3w59_full_validation.pdf.gz | 486.6 KB | Display | |
Data in XML | 3w59_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 3w59_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w59 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w59 | HTTPS FTP |
-Related structure data
Related structure data | 3w58C 1gzwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14599.477 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 3.25 Å3/Da / Density % sol: 62.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 2.0M ammonium sulfate, 1% 2-Mercaptoethanol, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 29, 2011 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.19 Å / Num. all: 45407 / Num. obs: 45407 / % possible obs: 100 % / Biso Wilson estimate: 17.86 Å2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 11.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GZW Resolution: 2.1→47.19 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.9227 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.03 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→47.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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