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- PDB-3bav: Crystal structure of L26A/D28N mutant of Human acidic fibroblast ... -

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Basic information

Entry
Database: PDB / ID: 3bav
TitleCrystal structure of L26A/D28N mutant of Human acidic fibroblast growth factor
ComponentsHeparin-binding growth factor 1
KeywordsHORMONE / beta-trefoil / Acetylation / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism
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
FORMIC ACID / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLee, J. / Blaber, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A logical OR redundancy within the Asx-Pro-Asx-Gly type I beta-turn motif.
Authors: Lee, J. / Dubey, V.K. / Longo, L.M. / Blaber, M.
History
DepositionNov 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 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: Heparin-binding growth factor 1
B: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5687
Polymers33,2872
Non-polymers2805
Water4,252236
1
A: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8324
Polymers16,6441
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7363
Polymers16,6441
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.777, 96.950, 108.225
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 Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 16643.682 Da / Num. of mol.: 2 / Mutation: L26A, D28N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: PET21a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 58.25 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.3M Na-formate, 0.4M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2006 / Details: double flat Si crystal monochromator
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→28.56 Å / Num. all: 49198 / Num. obs: 44914 / % possible obs: 91.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 44.62
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 3 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.34 / Num. unique all: 4220 / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1JQZ

1jqz


Resolution: 1.62→28.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 172126.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2266 5 %RANDOM
Rwork0.193 ---
obs0.193 44914 89.3 %-
all-49198 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6163 Å2 / ksol: 0.399468 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--2.79 Å20 Å2
3----3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.62→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 5 248 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 250 4.8 %
Rwork0.228 4913 -
obs-4913 62.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5formate.paramformate.top

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