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

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Basic information

Entry
Database: PDB / ID: 1jtc
TitleHuman Acidic Fibroblast Growth Factor. 141 Amino Acid Form with Amino Terminal His Tag AND LEU 44 REPLACED BY PHE (L44F)
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 / FGFR4 ligand binding and activation / 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 / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / S100 protein binding / positive regulation of hepatocyte proliferation / 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 intracellular signal transduction / 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 / activation of protein kinase B activity / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / neurogenesis / Signaling by FGFR2 in disease / positive regulation of endothelial cell migration / Signaling by FGFR1 in disease / positive regulation of MAP kinase activity / Hsp70 protein binding / extracellular matrix / regulation of cell migration / epithelial cell proliferation / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / lung development / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / positive regulation of cholesterol biosynthetic process / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell cortex / angiogenesis / 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 / 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
FORMIC ACID / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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: 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
C: acidic fibroblast growth factor
D: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,25112
Polymers66,8834
Non-polymers3688
Water7,819434
1
A: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8133
Polymers16,7211
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8133
Polymers16,7211
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8133
Polymers16,7211
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8133
Polymers16,7211
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.923, 73.784, 109.131
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16720.764 Da / Num. of mol.: 4 / Mutation: L44F
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 57.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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: Jul 10, 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: 1.7→36.9 Å / Num. all: 85721 / Num. obs: 85721 / % possible obs: 88.2 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 1.2 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.6 / % possible all: 69.1
Reflection
*PLUS
Num. obs: 72647 / % possible obs: 88.1 % / Num. measured all: 274969
Reflection shell
*PLUS
% possible obs: 64.8 % / Mean I/σ(I) obs: 2.7

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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: 1.7→36.9 Å / Isotropic thermal model: TRONRUD / Stereochemistry target values: TRONRUD
Num. reflection% reflectionSelection details
all85721 --
obs65452 76.4 %-
Rfree--RANDOM
Solvent computationSolvent model: TNT / Bsol: 248.83 Å2 / ksol: 0.977 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4538 0 0 458 4996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_dihedral_angle_d11.2
LS refinement shellResolution: 1.7→1.73 Å /
RfactorNum. reflection
Rfree0.31 544
Rwork0.29 -
obs-4876
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Num. reflection Rfree: 7195 / % reflection Rfree: 10 % / Rfactor all: 0.197 / Rfactor obs: 0.193 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg11.2

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