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- PDB-4q9p: Crystal structure of C16T/K12V/C117V/P134V mutant of human acidic... -

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Basic information

Entry
Database: PDB / ID: 4q9p
TitleCrystal structure of C16T/K12V/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 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / 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 / positive regulation of hepatocyte proliferation / 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 intracellular signal transduction / 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 / activation of protein kinase B activity / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / neurogenesis / Signaling by FGFR2 in disease / positive regulation of endothelial cell migration / Signaling by FGFR1 in disease / positive regulation of MAP kinase activity / extracellular matrix / Hsp70 protein binding / regulation of cell migration / epithelial cell proliferation / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / lung development / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / positive regulation of cholesterol biosynthetic process / 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 / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell cortex / angiogenesis / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3052
Polymers33,3052
Non-polymers00
Water5,026279
1
A: Fibroblast growth factor 1


Theoretical massNumber of molelcules
Total (without water)16,6531
Polymers16,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor 1


Theoretical massNumber of molelcules
Total (without water)16,6531
Polymers16,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.687, 53.687, 217.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 16652.662 Da / Num. of mol.: 2 / Fragment: UNP residues 16-155 / Mutation: K12V/C16T/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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0 M sodium citrate, 0.1 M imidazole, pH 8.0, 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: 1.8→50 Å / Num. obs: 29447 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.8 Å

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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: 1.8→38.244 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 1469 5 %
Rwork0.1731 --
obs0.1749 29357 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 0 279 2454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062242
X-RAY DIFFRACTIONf_angle_d1.0313036
X-RAY DIFFRACTIONf_dihedral_angle_d13.224839
X-RAY DIFFRACTIONf_chiral_restr0.044326
X-RAY DIFFRACTIONf_plane_restr0.005393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-1.86430.24221130.18982139X-RAY DIFFRACTION76
1.8643-1.93890.20661310.18542504X-RAY DIFFRACTION87
1.9389-2.02710.24581410.18922673X-RAY DIFFRACTION94
2.0271-2.1340.2411490.18712837X-RAY DIFFRACTION99
2.134-2.26770.21531520.18222869X-RAY DIFFRACTION100
2.2677-2.44280.20681510.19082882X-RAY DIFFRACTION99
2.4428-2.68850.27131530.20122889X-RAY DIFFRACTION99
2.6885-3.07740.21431530.1832924X-RAY DIFFRACTION100
3.0774-3.87660.19131580.15682995X-RAY DIFFRACTION100
3.8766-38.25290.18491680.15343176X-RAY DIFFRACTION100

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