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- PDB-1jt3: Human Acidic Fibroblast Growth Factor. 141 Amino Acid Form with A... -

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Basic information

Entry
Database: PDB / ID: 1jt3
TitleHuman Acidic Fibroblast Growth Factor. 141 Amino Acid Form with Amino Histidine Tag AND LEU 73 REPLACED BY VAL (L73V)
Componentsacidic fibroblast growth factor
KeywordsHORMONE/GROWTH FACTOR / beta-trefoil / HORMONE-GROWTH FACTOR COMPLEX
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 / 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 / S100 protein binding / 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 MAP kinase activity / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / 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 / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / neurogenesis / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / extracellular matrix / positive regulation of endothelial cell migration / lung development / regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / wound healing / positive regulation of cholesterol biosynthetic process / integrin binding / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heparin binding / cellular response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell cortex / 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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBrych, S.R. / Blaber, S.I. / Logan, T.M. / Blaber, M.
CitationJournal: Protein Sci. / Year: 2001
Title: Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.
Authors: Brych, S.R. / Blaber, S.I. / Logan, T.M. / Blaber, M.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acidic fibroblast growth factor
B: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6345
Polymers33,3452
Non-polymers2883
Water3,585199
1
A: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8653
Polymers16,6731
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7692
Polymers16,6731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: acidic fibroblast growth factor
hetero molecules

B: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6345
Polymers33,3452
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area1980 Å2
ΔGint-55 kcal/mol
Surface area12140 Å2
MethodPISA, PQS
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.316, 97.903, 108.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein acidic fibroblast growth factor / HEPARIN-BINDING GROWTH FACTOR 1 / HBGF-1 / AFGF


Mass: 16672.721 Da / Num. of mol.: 2 / Mutation: L73V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05230
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.96 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium formate, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 4 or 10 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19-12 mg/mlprotein1drop
23.4-4.4 Msodium formate1reservoir
31.0-1.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 16, 2000 / Details: Osmic Blue Confocal mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→39.9 Å / Num. all: 28903 / Num. obs: 27633 / % possible obs: 98.8 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 7.2 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 22.2
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.7 / % possible all: 87.5
Reflection
*PLUS
Num. measured all: 281913
Reflection shell
*PLUS
% possible obs: 87.5 %

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Processing

Software
NameClassification
MRCHKmodel building
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
MRCHKphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JQZ

1jqz


Resolution: 1.95→39.9 Å / Isotropic thermal model: TRONRUD / Stereochemistry target values: TRONRUD
Num. reflection% reflectionSelection details
all27633 --
obs24920 86.2 %-
Rfree--RANDOM
Solvent computationSolvent model: TNT / Bsol: 227 Å2 / ksol: 0.916 e/Å3
Refinement stepCycle: LAST / Resolution: 1.95→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 15 199 2494
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.5
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_dihedral_angle_d10.3
LS refinement shellResolution: 1.95→1.98 Å /
RfactorNum. reflection
Rfree0.34 259
Rwork0.31 -
obs-2239
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2713 / % reflection Rfree: 10 % / Rfactor all: 0.219 / Rfactor obs: 0.214 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg10.3

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