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Yorodumi- PDB-3bag: Crystal structure of K112N/N114A mutant of Human acidic fibroblas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bag | ||||||
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Title | Crystal structure of K112N/N114A 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lee, J. / Blaber, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: A logical OR redundancy within the Asx-Pro-Asx-Gly type I beta-turn motif. Authors: Lee, J. / Dubey, V.K. / Longo, L.M. / Blaber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bag.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bag.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bag_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 3bag_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 3bag_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3bag_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/3bag ftp://data.pdbj.org/pub/pdb/validation_reports/ba/3bag | HTTPS FTP |
-Related structure data
Related structure data | 3b9uC 3ba4C 3ba5C 3ba7C 3badC 3bahC 3baoC 3baqC 3bauC 3bavC 3bb2C 1jqzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16628.645 Da / Num. of mol.: 2 / Mutation: K112N, N114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: PET21a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230 #2: Chemical | ChemComp-FMT / #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: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.8M Na-formate, 0.2M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2006 / Details: double flat Si crystal monochromator |
Radiation | Monochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→35.6 Å / Num. all: 40673 / Num. obs: 37121 / % possible obs: 91.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 30.47 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4.29 / Num. unique all: 4007 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1JQZ Resolution: 1.75→35.6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 114656 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.3753 Å2 / ksol: 0.377246 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→35.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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