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- PDB-1nzk: Crystal Structure of a Multiple Mutant (L44F, L73V, V109L, L111I,... -

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Basic information

Entry
Database: PDB / ID: 1nzk
TitleCrystal Structure of a Multiple Mutant (L44F, L73V, V109L, L111I, C117V) of Human Acidic Fibroblast Growth Factor
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
FORMIC ACID / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBrych, S.R. / Kim, J. / Logan, T.M. / Blaber, M.
CitationJournal: Protein Sci. / Year: 2003
Title: Accommodation of a highly symmetric core within a symmetric protein superfold.
Authors: Brych, S.R. / Kim, J. / Logan, T.M. / Blaber, M.
History
DepositionFeb 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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)66,46216
Polymers65,7104
Non-polymers75212
Water7,873437
1
A: Acidic Fibroblast Growth Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6164
Polymers16,4281
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acidic Fibroblast Growth Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6164
Polymers16,4281
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acidic Fibroblast Growth Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6164
Polymers16,4281
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acidic Fibroblast Growth Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6164
Polymers16,4281
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.747, 74.033, 109.085
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
Acidic Fibroblast Growth Factor / Heparin-binding growth factor 1 / HBGF-1 / AFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 16427.506 Da / Num. of mol.: 4 / Mutation: L44F, L73V, V109L, L111I, C117V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1 / 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.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.79 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium Formate, Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 21, 2002 / Details: Osmic purple 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→29.6 Å / Num. all: 57055 / Num. obs: 55365 / % possible obs: 97 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 1.45 / Redundancy: 5.3 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.8
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JT7

1jt7


Resolution: 1.95→29.6 Å / Cross valid method: THROUGHOUT / σ(F): 2.9
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1677 3.1 %RANDOM
Rwork0.194 ---
obs0.196 53688 97 %-
all-57055 --
Refinement stepCycle: LAST / Resolution: 1.95→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 20 461 4999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.6
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_dihedral_angle_d11
LS refinement shellResolution: 1.95→1.98 Å /
RfactorNum. reflection
Rfree0.27 188
Rwork0.25 -
obs-1677

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