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- PDB-2j3p: crystal structure of rat FGF1 at 1.4 A -

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Basic information

Entry
Database: PDB / ID: 2j3p
Titlecrystal structure of rat FGF1 at 1.4 A
ComponentsHEPARIN-BINDING GROWTH FACTOR 1
KeywordsGROWTH FACTOR / DEVELOPMENTAL PROTEIN / ACIDIC FIBROBLAST GROWTH FACTOR / DIFFERENTIATION / HEPARIN-BINDING / MITOGEN / CYTOKINE / ANGIOGENESIS / BETA-TREFOIL
Function / homology
Function and homology information


FGFR4 ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR2c ligand binding and activation / Downstream signaling of activated FGFR1 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling ...FGFR4 ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR2c ligand binding and activation / Downstream signaling of activated FGFR1 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / FGFR2b ligand binding and activation / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / PI-3K cascade:FGFR2 / PI3K Cascade / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / organ induction / positive regulation of hepatocyte proliferation / S100 protein binding / RAF/MAP kinase cascade / positive regulation of intracellular signal transduction / positive regulation of sprouting angiogenesis / positive regulation of cell division / fibroblast growth factor receptor signaling pathway / Hsp70 protein binding / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / positive regulation of epithelial cell proliferation / animal organ morphogenesis / growth factor activity / lung development / wound healing / positive regulation of angiogenesis / integrin binding / heparin binding / cellular response to heat / cell cortex / angiogenesis / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / positive regulation of gene expression / 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 speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKulahin, N. / Kristensen, O. / Berezin, V. / Gajhede, M. / Bock, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of Rat Acidic Fibroblast Growth Factor at 1.4 A Resolution.
Authors: Kulahin, N. / Kiselyov, V. / Kochoyan, A. / Kristensen, O. / Kastrup, J.S. / Berezin, V. / Bock, E. / Gajhede, M.
History
DepositionAug 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8327
Polymers30,3522
Non-polymers4805
Water4,594255
1
A: HEPARIN-BINDING GROWTH FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5605
Polymers15,1761
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEPARIN-BINDING GROWTH FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2722
Polymers15,1761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.882, 61.655, 88.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97657, -0.18425, -0.11121), (-0.14327, -0.17102, -0.97479), (0.16059, 0.96789, -0.19341)
Vector: 18.59949, 26.98759, -1.52201)

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Components

#1: Protein HEPARIN-BINDING GROWTH FACTOR 1 / ACIDIC FIBROBLAST GROWTH FACTOR / HBGF-1 / AFGF


Mass: 15176.041 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP 10 F' / References: UniProt: P61149
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.8 Å3/Da / Density % sol: 33 %
Crystal growpH: 5 / Details: 1.6 M AMMONIUM SULFATE, 0.1 M CITRIC ACID PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98
DetectorDate: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 47203 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.49 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7.73 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0016refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFC

1afc


Resolution: 1.4→50.64 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.066 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2383 5.1 %RANDOM
Rwork0.202 ---
obs0.204 44754 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 25 255 2396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9793094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08524.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96515409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0141513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021753
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2959
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21506
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7751.51414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29922216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9463973
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7454.5869
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 136
Rwork0.254 3327

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