[English] 日本語
Yorodumi- PDB-3fgm: Crystal structure of L44F/C83T/C117V/F132W mutant of Human acidic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fgm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of L44F/C83T/C117V/F132W mutant of Human acidic fibroblast growth factor | ||||||
Components | Heparin-binding growth factor 1 | ||||||
Keywords | HORMONE / beta-trefoil / Acetylation / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Blaber, M. / Lee, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The interaction between thermodynamic stability and buried free cysteines in regulating the functional half-life of fibroblast growth factor-1. Authors: Lee, J. / Blaber, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fgm.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fgm.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fgm_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3fgm_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 3fgm_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3fgm_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/3fgm ftp://data.pdbj.org/pub/pdb/validation_reports/fg/3fgm | HTTPS FTP |
-Related structure data
Related structure data | 3fj8C 3fj9C 3fjaC 3fjbC 3fjcC 3fjdC 1jqzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | monomer |
-Components
#1: Protein | Mass: 16753.748 Da / Num. of mol.: 2 / Mutation: L44F, C83T, C117V, F132W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05230 #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.44 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 4.1M Na-formate, 0.1M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 2008 / Details: OSMIC BLUE CONFOCAL MIRROR |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→28.88 Å / Num. all: 27994 / Num. obs: 26793 / % possible obs: 95.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 13.2 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 8.61 / Num. unique all: 1482 / % possible all: 78.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JQZ Resolution: 1.95→28.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 697341.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.2243 Å2 / ksol: 0.395398 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→28.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|