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- PDB-1bfg: CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 1bfg
TitleCRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTROMS RESOLUTION
ComponentsBASIC FIBROBLAST GROWTH FACTOR
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / chemokine binding / negative regulation of fibroblast growth factor receptor signaling pathway / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / positive regulation of stem cell differentiation / positive regulation of epithelial tube formation / hyaluronan catabolic process / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / glial cell differentiation / negative regulation of wound healing / inner ear auditory receptor cell differentiation / stem cell development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / embryonic morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / 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 / mammary gland epithelial cell differentiation / 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 / paracrine signaling / negative regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / Signaling by FGFR2 IIIa TM / positive regulation of DNA biosynthetic process / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR3 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / positive regulation of stem cell proliferation / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / chemoattractant activity / positive regulation of cell division / negative regulation of blood vessel endothelial cell migration / Non-integrin membrane-ECM interactions / PI3K Cascade / neuroblast proliferation / response to axon injury / canonical Wnt signaling pathway / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / regulation of angiogenesis / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / release of sequestered calcium ion into cytosol / FRS-mediated FGFR3 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / Signaling by FGFR2 in disease / substantia nigra development / ERK1 and ERK2 cascade / Signaling by FGFR1 in disease / positive regulation of endothelial cell migration / nuclear receptor coactivator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsKitagawa, Y. / Ago, H. / Katsube, Y. / Fujishima, A. / Matsuura, Y.
CitationJournal: J.Biochem.(Tokyo) / Year: 1991
Title: Crystal structure of basic fibroblast growth factor at 1.6 A resolution.
Authors: Ago, H. / Kitagawa, Y. / Fujishima, A. / Matsuura, Y. / Katsube, Y.
History
DepositionApr 15, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BASIC FIBROBLAST GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)16,4041
Polymers16,4041
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.370, 34.750, 30.890
Angle α, β, γ (deg.)94.55, 103.39, 88.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein BASIC FIBROBLAST GROWTH FACTOR /


Mass: 16403.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P09038
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %bFGF solution1drop
222 %(w/v)PEG40001reservoir
36.1 mM2-mercaptoethanol1reservoir
450 mMsodium citrate 1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 17537 / Num. measured all: 40624 / Rmerge F obs: 0.039

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→5 Å / σ(F): 3 /
RfactorNum. reflection
obs0.153 15265
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 99 1113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 5 Å / Num. reflection obs: 15265 / σ(F): 3 / Rfactor obs: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.7 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.011

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