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- PDB-1fga: REFINEMENT OF THE STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACT... -

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Basic information

Entry
Database: PDB / ID: 1fga
TitleREFINEMENT OF THE STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTROMS RESOLUTION AND ANALYSIS OF PRESUMED HEPARIN BINDING SITES BY SELENATE SUBSTITUTION
ComponentsBASIC FIBROBLAST GROWTH FACTOR
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / response to wortmannin / Formation of intermediate mesoderm / chondroblast differentiation ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / response to wortmannin / Formation of intermediate mesoderm / chondroblast differentiation / FGFRL1 modulation of FGFR1 signaling / negative regulation of fibroblast growth factor receptor signaling pathway / stem cell development / chemokine binding / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / angiogenesis involved in coronary vascular morphogenesis / Formation of the nephric duct / regulation of endothelial cell chemotaxis to fibroblast growth factor / negative regulation of wound healing / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / receptor-receptor interaction / hyaluronan catabolic process / fibroblast growth factor receptor binding / FGFR2b ligand binding and activation / embryonic morphogenesis / FGFR2c ligand binding and activation / FGFR4 ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of epithelial tube formation / 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 / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / paracrine signaling / negative regulation of fibroblast migration / behavioral response to ethanol / positive regulation of blood vessel branching / branching involved in ureteric bud morphogenesis / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / histone H3K9me2/3 reader activity / positive regulation of cell migration involved in sprouting angiogenesis / Signaling by FGFR2 IIIa TM / positive regulation of DNA biosynthetic process / Syndecan interactions / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / fibroblast growth factor receptor signaling pathway / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR1 / positive regulation of MAP kinase activity / chemoattractant activity / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / Non-integrin membrane-ECM interactions / PI3K Cascade / regulation of angiogenesis / positive regulation of blood vessel endothelial cell migration / positive regulation of cardiac muscle cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / SHC-mediated cascade:FGFR3 / neurogenesis / release of sequestered calcium ion into cytosol / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / stem cell proliferation / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / positive regulation of endothelial cell proliferation / Signaling by FGFR2 in disease / regulation of cell migration / animal organ morphogenesis / Signaling by FGFR1 in disease / positive regulation of endothelial cell migration / cytokine activity / wound healing / growth factor activity / Negative regulation of FGFR3 signaling / cellular response to mechanical stimulus / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / positive regulation of miRNA transcription / integrin binding / chemotaxis / positive regulation of angiogenesis
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
BETA-MERCAPTOETHANOL / SELENATE ION / Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsEriksson, A.E. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 1993
Title: Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution.
Authors: Eriksson, A.E. / Cousens, L.S. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Three-Dimensional Structure of Human Basic Fibroblast Growth Factor
Authors: Eriksson, A.E. / Cousens, L.S. / Weaver, L.H. / Matthews, B.W.
History
DepositionFeb 26, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 22, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / software / struct_conn
Item: _diffrn.ambient_pressure / _diffrn.ambient_temp ..._diffrn.ambient_pressure / _diffrn.ambient_temp / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_wavelength_list / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: BASIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8785
Polymers16,4361
Non-polymers4424
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.800, 33.500, 35.800
Angle α, β, γ (deg.)58.80, 72.40, 76.10
Int Tables number1
Space group name H-MP1
Atom site foot note1: SG SEO 69 IS BONDED TO SG CYS 69 AND SG SEO 92 IS BONDED TO SD CYS 92.

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Components

#1: Protein BASIC FIBROBLAST GROWTH FACTOR


Mass: 16435.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P09038
#2: Chemical ChemComp-SE4 / SELENATE ION


Mass: 142.958 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O4Se
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.48 %
Crystal grow
*PLUS
pH: 8.1 / Method: vapor diffusion / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.0 Mammonium sulfate12
20.1 MTris-HCl12
30.1 M12NaCl
40.1 %(v/v)BME12

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: rotating-anode X-ray tube / Type: RIGAKU RU200 / Target: Cu
DetectorType: AREA DETECTOR / Detector: AREA DETECTOR / Details: Xuong-Hamlin
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 2.2 Å / Num. all: 46606 / Num. obs: 13971 / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
TNTrefinement
Xengen (HOWARD, NIELSEN, XUONG)data scaling
RefinementResolution: 2.2→20 Å / Rfactor obs: 0.138
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 10 73 1085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg3.2
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rfactor obs: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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