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Yorodumi- PDB-1w6m: X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH GA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w6m | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH GALACTOSE | ||||||
Components | (GALECTIN-1) x 2 | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE-BINDING PROTEIN | ||||||
Function / homology | Function and homology information galectin complex / 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) / carbohydrate binding ...galectin complex / 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) / carbohydrate binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lopez-Lucendo, M.I.F. / Gabius, H.J. / Romero, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Growth-Regulatory Human Galectin-1: Crystallographic Characterisation of the Structural Changes Induced by Single-Site Mutations and Their Impact on the Thermodynamics of Ligand Binding. Authors: Lopez-Lucendo, M.I.F. / Solis, D. / Andre, S. / Hirabayashi, J. / Kasai, K. / Kaltner, H. / Gabius, H.J. / Romero, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w6m.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w6m.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1w6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/1w6m ftp://data.pdbj.org/pub/pdb/validation_reports/w6/1w6m | HTTPS FTP |
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-Related structure data
Related structure data | 1gzwSC 1w6nC 1w6oC 1w6pC 1w6qC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.3715, -0.35986, -0.85586), Vector: |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 14657.447 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PH14GAL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: P09382 |
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#2: Protein | Mass: 14641.447 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PH14GAL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: P09382 |
-Sugars , 1 types, 2 molecules
#5: Sugar |
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-Non-polymers , 3 types, 138 molecules
#3: Chemical | ChemComp-BME / #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | MAY REGULATE CELL APOPTOSIS AND CELL DIFFERENTIATION. ENGINEERED RESIDUE IN CHAIN A, CYS 2 TO SER ...MAY REGULATE CELL APOPTOSIS AND CELL DIFFERENTI |
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Sequence details | CYS 2 ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.6 Details: CRYSTALS WERE OBTAINED IN SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE AND 1% BETA-MERCAPTO ETHANOL, PH 5.6). ...Details: CRYSTALS WERE OBTAINED IN SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE AND 1% BETA-MERCAPTO ETHANOL, PH 5.6). THE GALACTOSE COMPLEX WAS OBTAINED BY SOAKING C2S CRYSTALS FOR 72H IN THE MOTHER LIQUOR SUPPLEMENTED WITH 10 MM OF GALACTOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25.6 Å / Num. obs: 13774 / % possible obs: 96.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.3→2.45 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.1 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZW Resolution: 2.3→25.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1341364.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6187 Å2 / ksol: 0.361353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→25.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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