+Open data
-Basic information
Entry | Database: PDB / ID: 1pwa | ||||||
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Title | Crystal structure of Fibroblast Growth Factor 19 | ||||||
Components | Fibroblast growth factor-19 | ||||||
Keywords | HORMONE/GROWTH FACTOR / BETA TREFOIL / DISULPHIDE BONDS / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling ...negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling / regulation of cell migration / positive regulation of glucose import / Negative regulation of FGFR4 signaling / animal organ morphogenesis / positive regulation of JNK cascade / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Harmer, N.J. / Pellegrini, L. / Chirgadze, D. / Fernandez-Recio, J. / Blundell, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: The crystal structure of fibroblast growth factor (FGF) 19 reveals novel features of the FGF family and offers a structural basis for its unusual receptor affinity. Authors: Harmer, N.J. / Pellegrini, L. / Chirgadze, D. / Fernandez-Recio, J. / Blundell, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pwa.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pwa.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pwa_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 1pwa_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 1pwa_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1pwa_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwa ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwa | HTTPS FTP |
-Related structure data
Related structure data | 1ihkS 1ijtS 1jqzS 1qqkS 2fgfS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18116.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF19 / Plasmid: pGAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: O95750 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-TRS / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, potassium phosphate, magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2003 / Details: mirrors |
Radiation | Monochromator: Rh coated silica / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→25 Å / Num. all: 42313 / % possible obs: 99.9 % / Redundancy: 12.08 % / Biso Wilson estimate: 13.695 Å2 / Rsym value: 0.062 / Net I/σ(I): 36.5 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 4.32 / Num. unique all: 2080 / Rsym value: 0.586 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 23.33 Å / Num. obs: 42303 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 4.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1JQZ, 2FGF, 1IJT, 1QQK, 1IHK Resolution: 1.3→23.33 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 0.508 / SU ML: 0.022 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.373 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→23.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.298→1.332 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 1.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.181 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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