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- PDB-1bar: THREE-DIMENSIONAL STRUCTURES OF ACIDIC AND BASIC FIBROBLAST GROWT... -

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Basic information

Entry
Database: PDB / ID: 1bar
TitleTHREE-DIMENSIONAL STRUCTURES OF ACIDIC AND BASIC FIBROBLAST GROWTH FACTORS
ComponentsACIDIC FIBROBLAST GROWTH FACTORFGF1
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR1c ligand binding and activation / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR2 / Phospholipase C-mediated cascade; FGFR3 ...FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR1c ligand binding and activation / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR2 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Downstream signaling of activated FGFR1 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / RAF/MAP kinase cascade / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI3K Cascade / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / S100 protein binding / positive regulation of intracellular signal transduction / positive regulation of sprouting angiogenesis / positive regulation of cell division / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / positive regulation of endothelial cell migration / positive regulation of epithelial cell proliferation / animal organ morphogenesis / growth factor activity / lung development / wound healing / positive regulation of angiogenesis / integrin binding / heparin binding / cellular response to heat / cell cortex / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsZhu, X. / Komiya, H. / Chirino, A. / Faham, S. / Fox, G.M. / Arakawa, T. / Hsu, B.T. / Rees, D.C.
CitationJournal: Science / Year: 1991
Title: Three-dimensional structures of acidic and basic fibroblast growth factors.
Authors: Zhu, X. / Komiya, H. / Chirino, A. / Faham, S. / Fox, G.M. / Arakawa, T. / Hsu, B.T. / Rees, D.C.
History
DepositionSep 29, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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

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Assembly

Deposited unit
A: ACIDIC FIBROBLAST GROWTH FACTOR
B: ACIDIC FIBROBLAST GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)31,5802
Polymers31,5802
Non-polymers00
Water64936
1
A: ACIDIC FIBROBLAST GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)15,7901
Polymers15,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACIDIC FIBROBLAST GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)15,7901
Polymers15,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ACIDIC FIBROBLAST GROWTH FACTOR
B: ACIDIC FIBROBLAST GROWTH FACTOR

A: ACIDIC FIBROBLAST GROWTH FACTOR
B: ACIDIC FIBROBLAST GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)63,1604
Polymers63,1604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6410 Å2
ΔGint-32 kcal/mol
Surface area19560 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-14 kcal/mol
Surface area11140 Å2
MethodPISA
5
B: ACIDIC FIBROBLAST GROWTH FACTOR

B: ACIDIC FIBROBLAST GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)31,5802
Polymers31,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1310 Å2
ΔGint-8 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.600, 78.600, 115.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ACIDIC FIBROBLAST GROWTH FACTOR / FGF1


Mass: 15789.911 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P03968
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %PEG80001reservoir
25 %methylpentanediol1reservoir
30.1 MHEPES1reservoir
49 mg/mlbFGF solution1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 0 36 2088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.3

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