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Yorodumi- PDB-3jut: Acidic Fibroblast Growth Factor (FGF-1) complexed with gentisic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jut | ||||||
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Title | Acidic Fibroblast Growth Factor (FGF-1) complexed with gentisic acid | ||||||
Components | Heparin-binding growth factor 1 | ||||||
Keywords | HORMONE / GROWTH FACTOR / FGF-1 INHIBITORS / Angiogenesis / Developmental protein / Differentiation / Heparin-binding / Mitogen | ||||||
Function / homology | Function and homology information mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of hepatocyte proliferation / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / Hsp70 protein binding / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / animal organ morphogenesis / Negative regulation of FGFR1 signaling / growth factor activity / positive regulation of MAP kinase activity / lung development / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Fernandez, I.S. / Gimenez-Gallego, G. / Romero, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Gentisic acid, a compound associated with plant defense and a metabolite of aspirin, heads a new class of in vivo fibroblast growth factor inhibitors. Authors: Fernandez, I.S. / Cuevas, P. / Angulo, J. / Lopez-Navajas, P. / Canales-Mayordomo, A. / Gonzalez-Corrochano, R. / Lozano, R.M. / Valverde, S. / Jimenez-Barbero, J. / Romero, A. / Gimenez-Gallego, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jut.cif.gz | 162 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jut.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 3jut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jut_validation.pdf.gz | 490.4 KB | Display | wwPDB validaton report |
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Full document | 3jut_full_validation.pdf.gz | 518.6 KB | Display | |
Data in XML | 3jut_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 3jut_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/3jut ftp://data.pdbj.org/pub/pdb/validation_reports/ju/3jut | HTTPS FTP |
-Related structure data
Related structure data | 3k1xC 1axmS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6 / Auth seq-ID: 1 - 130 / Label seq-ID: 1 - 130
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-Components
#1: Protein | Mass: 14752.703 Da / Num. of mol.: 6 / Fragment: Heparin-binding, UNP residues 24-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRAT-4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P05230 #2: Chemical | #3: 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: 2.48 Å3/Da / Density % sol: 50.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: Equal volumes of protein and inhibitor solutions, 0.75 and 1.5 mM,respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5 mM sodium phosphate [pH 7.8]. ...Details: Equal volumes of protein and inhibitor solutions, 0.75 and 1.5 mM,respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5 mM sodium phosphate [pH 7.8]. The drops were equilibrated against 200 ml of 1.3M Li2SO4 and typical crystals grew within two weeks , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→47.7 Å / Num. all: 42342 / Num. obs: 41838 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 31.73 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 1.6 / Num. unique all: 5625 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1axm Resolution: 2.25→37.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.715 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.346 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→37.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1031 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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