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- PDB-4yol: Human fibroblast growth factor-1 C16S/A66C/C117A/P134A -

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Basic information

Entry
Database: PDB / ID: 4yol
TitleHuman fibroblast growth factor-1 C16S/A66C/C117A/P134A
ComponentsFibroblast growth factor 1FGF1
KeywordsPROTEIN BINDING / fibroblast growth factor-1 / cysteine-free mutant / FGF-1 / intramolecular disulfide
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 / extracellular matrix / Signaling by FGFR1 in disease / activation of protein kinase B activity / 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
CITRATE ANION / IMIDAZOLE / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.97 Å
AuthorsXia, X. / Blaber, M.
CitationJournal: J.Pharm.Sci. / Year: 2016
Title: Engineering a Cysteine-Free Form of Human Fibroblast Growth Factor-1 for "Second Generation" Therapeutic Application.
Authors: Xia, X. / Kumru, O.S. / Blaber, S.I. / Middaugh, C.R. / Li, L. / Ornitz, D.M. / Sutherland, M.A. / Tenorio, C.A. / Blaber, M.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Feb 13, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.host_org_common_name ..._citation.journal_id_CSD / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9995
Polymers33,5522
Non-polymers4473
Water5,783321
1
A: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0343
Polymers16,7761
Non-polymers2582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9652
Polymers16,7761
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.630, 97.831, 107.914
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
11B-344-

HOH

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Components

#1: Protein Fibroblast growth factor 1 / FGF1 / 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: 16775.842 Da / Num. of mol.: 2 / Fragment: UNP residues 16-155 / Mutation: C16S/A66C/C117A/P134A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Atlantibacter hermannii (bacteria) / References: UniProt: P05230
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.7 M sodium citrate, 0.1 M imidazole, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 28191 / % possible obs: 97.7 % / Redundancy: 9.7 % / Net I/σ(I): 39
Reflection shellResolution: 1.97→2 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.97→37.815 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 1998 7.1 %
Rwork0.1598 --
obs0.1625 28135 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→37.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 31 321 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072475
X-RAY DIFFRACTIONf_angle_d1.063351
X-RAY DIFFRACTIONf_dihedral_angle_d14.119928
X-RAY DIFFRACTIONf_chiral_restr0.045339
X-RAY DIFFRACTIONf_plane_restr0.005446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9615-2.01050.22831260.19171679X-RAY DIFFRACTION89
2.0105-2.06490.24171450.17411890X-RAY DIFFRACTION99
2.0649-2.12570.20861450.15851890X-RAY DIFFRACTION99
2.1257-2.19430.18831430.16051869X-RAY DIFFRACTION99
2.1943-2.27270.21031440.16761874X-RAY DIFFRACTION99
2.2727-2.36370.20881450.16721892X-RAY DIFFRACTION99
2.3637-2.47120.20721430.17031880X-RAY DIFFRACTION98
2.4712-2.60150.21291440.18941868X-RAY DIFFRACTION98
2.6015-2.76440.22421430.17151871X-RAY DIFFRACTION98
2.7644-2.97780.20971440.17421884X-RAY DIFFRACTION98
2.9778-3.27730.21351440.16021891X-RAY DIFFRACTION97
3.2773-3.75120.19171430.14471873X-RAY DIFFRACTION97
3.7512-4.72460.15191430.13211877X-RAY DIFFRACTION96
4.7246-37.8220.20121460.16291899X-RAY DIFFRACTION93

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