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- PDB-4q9g: Crystal structure of K12V/C16S/C117V/P134V mutant of human acidic... -

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Basic information

Entry
Database: PDB / ID: 4q9g
TitleCrystal structure of K12V/C16S/C117V/P134V mutant of human acidic fibroblast growth factor
ComponentsFibroblast growth factor 1
KeywordsPROTEIN BINDING / Beta-trefoil / growth factor / FGFR binding / heparin binding / extracellular matrix
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 / fibroblast growth factor receptor binding ...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 / 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 / S100 protein binding / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of sprouting angiogenesis / positive regulation of MAP kinase activity / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / activation of protein kinase B activity / 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 / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / neurogenesis / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / extracellular matrix / positive regulation of endothelial cell migration / lung development / regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / wound healing / positive regulation of cholesterol biosynthetic process / integrin binding / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heparin binding / cellular response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell cortex / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol
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
FORMIC ACID / PHOSPHATE ION / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.554 Å
AuthorsBlaber, M. / Xia, X.
CitationJournal: J.Pharm.Sci. / Year: 2015
Title: Mutation choice to eliminate buried free cysteines in protein therapeutics.
Authors: Xia, X. / Longo, L.M. / Blaber, M.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor 1
B: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5567
Polymers33,2772
Non-polymers2795
Water6,990388
1
A: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8264
Polymers16,6391
Non-polymers1873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7313
Polymers16,6391
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.395, 97.327, 108.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

21B-382-

HOH

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Components

#1: Protein Fibroblast growth factor 1 / FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / Heparin- ...FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / Heparin-binding growth factor 1 / HBGF-1


Mass: 16638.637 Da / Num. of mol.: 2 / Fragment: UNP residues 16-155 / Mutation: K12V/C16S/C117V/P134V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05230
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8 M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.02 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2013
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 55669 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 11.2 % / Num. unique all: 5160 / % possible all: 90.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Phaser MR)model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Phaser MR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.554→36.18 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 1999 3.59 %
Rwork0.1699 --
obs0.171 55659 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.554→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 17 388 2695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022383
X-RAY DIFFRACTIONf_angle_d1.7613224
X-RAY DIFFRACTIONf_dihedral_angle_d15.123882
X-RAY DIFFRACTIONf_chiral_restr0.11338
X-RAY DIFFRACTIONf_plane_restr0.011419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.554-1.59250.23331220.20923291X-RAY DIFFRACTION84
1.5925-1.63560.22721410.19583770X-RAY DIFFRACTION96
1.6356-1.68370.24221410.18283783X-RAY DIFFRACTION96
1.6837-1.7380.21491410.17673764X-RAY DIFFRACTION97
1.738-1.80010.2171430.183846X-RAY DIFFRACTION97
1.8001-1.87220.21111420.18463814X-RAY DIFFRACTION97
1.8722-1.95740.20461410.17643798X-RAY DIFFRACTION97
1.9574-2.06060.23331440.18163865X-RAY DIFFRACTION98
2.0606-2.18970.20741440.16773863X-RAY DIFFRACTION98
2.1897-2.35870.21121450.17023897X-RAY DIFFRACTION98
2.3587-2.5960.18251460.18093899X-RAY DIFFRACTION99
2.596-2.97150.21261470.17673942X-RAY DIFFRACTION99
2.9715-3.74320.18231480.1614001X-RAY DIFFRACTION99
3.7432-36.18960.17351540.1514127X-RAY DIFFRACTION99

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