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- PDB-1jt7: Human Acidic Fibroblast Growth Factor. 141 Amino Acid Form with A... -

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Basic information

Entry
Database: PDB / ID: 1jt7
TitleHuman Acidic Fibroblast Growth Factor. 141 Amino Acid Form with Amino Terminal His Tag AND LEU 44 REPLACED BY PHE AND LEU 73 REPLACED BY VAL AND VAL 109 REPLACED BY LEU (L44F/L73V/V109L)
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 / activation of protein kinase B activity / positive regulation of MAP kinase 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 / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / neurogenesis / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / extracellular matrix / Hsp70 protein binding / positive regulation of endothelial cell migration / 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 / wound healing / positive regulation of cholesterol biosynthetic process / 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

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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)67,35910
Polymers66,8834
Non-polymers4766
Water8,269459
1
A: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8633
Polymers16,7211
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8172
Polymers16,7211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8633
Polymers16,7211
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8172
Polymers16,7211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.540, 73.940, 108.920
Angle α, β, γ (deg.)90.00, 90.00, 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,L73V,V109L
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.95 Å3/Da / Density % sol: 57.66 %
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: Feb 22, 2001 / 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→30.9 Å / Num. all: 85399 / Num. obs: 85399 / % possible obs: 87.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.5
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.1 / % possible all: 47.1
Reflection
*PLUS
Num. obs: 71811 / Num. measured all: 455187
Reflection shell
*PLUS
% possible obs: 78.1 %

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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→30.9 Å / Isotropic thermal model: TRONRUD / Stereochemistry target values: TRONRUD
Num. reflection% reflectionSelection details
all85399 --
obs64706 75.8 %-
Rfree--RANDOM
Solvent computationSolvent model: TNT / Bsol: 187.39 Å2 / ksol: 0.857 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 20 465 5019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.7
X-RAY DIFFRACTIONt_bond_d0.007
X-RAY DIFFRACTIONt_dihedral_angle_d11.1
LS refinement shellResolution: 1.7→1.73 Å /
RfactorNum. reflection
Rfree0.27 371
Rwork0.27 -
obs-3471
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 7105 / % reflection Rfree: 10 % / Rfactor all: 0.196 / Rfactor obs: 0.192 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg11.1

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