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- PDB-1q03: Crystal structure of FGF-1, S50G/V51G mutant -

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Basic information

Entry
Database: PDB / ID: 1q03
TitleCrystal structure of FGF-1, S50G/V51G mutant
ComponentsHeparin-binding growth factor 1
Keywordshormone/growth factor / beta-trefoil / hormone-growth factor COMPLEX
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 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / 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 / Hsp70 protein binding / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / activation of protein kinase B activity / extracellular matrix / positive regulation of endothelial cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / animal organ morphogenesis / lung development / growth factor activity / positive regulation of MAP kinase activity / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / cellular response to heat / heparin binding / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell differentiation / positive regulation of ERK1 and ERK2 cascade / 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 / cytosol / cytoplasm
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKim, J. / Blaber, M.
CitationJournal: Protein Sci. / Year: 2005
Title: Sequence swapping does not result in conformation swapping for the beta4/beta5 and beta8/beta9 beta-hairpin turns in human acidic fibroblast growth factor
Authors: Kim, J. / Lee, J. / Brych, S.R. / Logan, T.M. / Blaber, M.
History
DepositionJul 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heparin-binding growth factor 1
B: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)33,2292
Polymers33,2292
Non-polymers00
Water2,324129
1
A: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)16,6151
Polymers16,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)16,6151
Polymers16,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.9, 97.0, 108.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein Heparin-binding growth factor 1 / Acidic fibroblast growth factor / FGF-1 / HBGF-1 / AFGF / Beta-endothelial cell growth factor / ...Acidic fibroblast growth factor / FGF-1 / HBGF-1 / AFGF / Beta-endothelial cell growth factor / ECGF-beta / fibroblast growth factor 1


Mass: 16614.643 Da / Num. of mol.: 2 / Mutation: S50G, V51G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05230
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2003 / Details: Osmic Purple confocal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→19.44 Å / Num. all: 25055 / Num. obs: 20665 / % possible obs: 82.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JQZ

1jqz


Resolution: 2.05→19.44 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.227 995 4.8 %random
Rwork0.197 ---
obs0.1971 20665 --
all-25055 --
Refinement stepCycle: LAST / Resolution: 2.05→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 129 2384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.05→2.1 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection
Rfree0.229 120
Rwork0.173 -
obs-2406

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