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- PDB-3bah: Crystal structure of K112N mutant of Human acidic fibroblast grow... -

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Basic information

Entry
Database: PDB / ID: 3bah
TitleCrystal structure of K112N 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 / FGFR2b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / Signaling by activated point mutants of FGFR3 ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / FGFR2b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / organ induction / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / S100 protein binding / positive regulation of hepatocyte proliferation / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR1 in disease / Hsp70 protein binding / activation of protein kinase B activity / regulation of cell migration / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / animal organ morphogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / lung development / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / growth factor activity / positive regulation of MAP kinase activity / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cell cortex / cellular response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 7, 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)33,80412
Polymers33,3432
Non-polymers46010
Water4,972276
1
A: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9487
Polymers16,6721
Non-polymers2766
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)16,8565
Polymers16,6721
Non-polymers1844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.407, 96.317, 108.233
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: 16671.670 Da / Num. of mol.: 2 / Mutation: K112N
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 58.26 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.9M Na-formate, 1.0M (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: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2006 / Details: double 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: 1.65→37.7 Å / Num. all: 47940 / Num. obs: 43314 / % possible obs: 90.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 45.57
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.63 / Num. unique all: 4748 / % possible all: 99.9

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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: 1.65→37.7 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 195127.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2171 5 %RANDOM
Rwork0.187 ---
obs0.187 43314 90.8 %-
all-47940 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.37 Å2 / ksol: 0.379647 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--3.67 Å20 Å2
3----3.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.65→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 0 306 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
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_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 257 4.5 %
Rwork0.212 5427 -
obs-5427 72.2 %
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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