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- PDB-3o3q: Crystal structure of "L44F/M67I/L73V/A103G/deletion 104-106/F108Y... -

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Basic information

Entry
Database: PDB / ID: 3o3q
TitleCrystal structure of "L44F/M67I/L73V/A103G/deletion 104-106/F108Y/V109L/L111I/C117V/R119G/deletion 120-122" mutant form of Human acidic fibroblast growth factor
ComponentsHeparin-binding growth factor 1
KeywordsHeparin-binding protein / beta-trefoil
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
Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLee, J. / Blaber, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: A polypeptide "building block"top-down symmetric deconstruction".
Authors: Lee, J. / Blaber, S.I. / Dubey, V.K. / Blaber, M.
History
DepositionJul 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparin-binding growth factor 1
B: Heparin-binding growth factor 1
C: Heparin-binding growth factor 1
D: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8516
Polymers63,6674
Non-polymers1842
Water10,413578
1
A: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)15,9171
Polymers15,9171
Non-polymers00
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)16,0092
Polymers15,9171
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)15,9171
Polymers15,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0092
Polymers15,9171
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.920, 56.890, 61.920
Angle α, β, γ (deg.)64.94, 89.76, 71.27
Int Tables number1
Space group name H-MP1

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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: 15916.790 Da / Num. of mol.: 4
Mutation: L44F, M67I, L73V, A103G, deletion 104-106, F108Y, V109L, L111I, C117V, R119G, deletion 120-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: PET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05230
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M magnesium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 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: 1.6→50 Å / Num. all: 68593 / Num. obs: 66029 / % possible obs: 96.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.83 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 30.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.86 / Num. unique all: 6304 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JQZ

1jqz


Resolution: 1.6→27.713 Å / SU ML: 1.04 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 3367 5.1 %random
Rwork0.1703 ---
obs0.1719 66029 92.06 %-
all-68593 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.866 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6443 Å2-0.8771 Å2-1.8405 Å2
2--0.9719 Å2-0.9531 Å2
3----2.6162 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 12 578 4556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064084
X-RAY DIFFRACTIONf_angle_d1.0065525
X-RAY DIFFRACTIONf_dihedral_angle_d15.4391475
X-RAY DIFFRACTIONf_chiral_restr0.067590
X-RAY DIFFRACTIONf_plane_restr0.005712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6-1.65650.23862910.19775061506174
1.6565-1.72280.22993240.18655934593487
1.7228-1.80120.23433120.17546092609290
1.8012-1.89610.2123370.17466234623491
1.8961-2.01490.20843410.1726272627293
2.0149-2.17040.21293790.16626431643195
2.1704-2.38870.21213350.1686547654796
2.3887-2.73410.21823230.18266659665997
2.7341-3.44370.20033620.16636691669198
3.4437-27.71670.17033630.15666741674199

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