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- PDB-1k5v: Human acidic fibroblast growth factor. 141 amino acid form with a... -

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Basic information

Entry
Database: PDB / ID: 1k5v
TitleHuman acidic fibroblast growth factor. 141 amino acid form with amino terminal His tag with Asn106 replaced by Gly (N106G).
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 / 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 / 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: 2.1 Å
AuthorsKim, J. / Blaber, S.I. / Blaber, M.
CitationJournal: Protein Sci. / Year: 2002
Title: Alternative type I and I' turn conformations in the beta8/beta9 beta-hairpin of human acidic fibroblast growth factor.
Authors: Kim, J. / Blaber, S.I. / Blaber, M.
History
DepositionOct 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4524
Polymers33,2592
Non-polymers1922
Water1,45981
1
A: Acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7262
Polymers16,6301
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acidic fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7262
Polymers16,6301
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.600, 60.120, 101.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acidic fibroblast growth factor


Mass: 16629.697 Da / Num. of mol.: 2 / Mutation: N106G
Source method: isolated from a genetically manipulated source
Details: AMINO TERMINAL HIS TAG / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG20,000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mMNaPi1drop
20.1 M1dropNaCl
310 mMammonium sulfate1drop
40.5 mMEDTA1drop
52 mMdithiothreitol1drop
620 %PEG200001reservoir
70.1 MMES1reservoirpH6.5

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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: Apr 11, 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: 2.1→29.4 Å / Num. all: 17283 / Num. obs: 16574 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 44.1
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 10.8 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 14287 / % possible obs: 97.4 % / Num. measured all: 245767 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 94.6 % / Mean I/σ(I) obs: 10.9

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Processing

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

1jqz


Resolution: 2.1→29.4 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: TRONRUD
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1652 10 %RANDOM
Rwork0.226 ---
all0.234 17283 --
obs0.234 14922 86 %-
Refinement stepCycle: LAST / Resolution: 2.1→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 10 81 2071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.6
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_dihedral_angle_d16.1
LS refinement shellResolution: 2.1→2.15 Å /
RfactorNum. reflection
Rfree0.35 147
Rwork0.31 -
obs-1652
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.1

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