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- PDB-1pwa: Crystal structure of Fibroblast Growth Factor 19 -

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Basic information

Entry
Database: PDB / ID: 1pwa
TitleCrystal structure of Fibroblast Growth Factor 19
ComponentsFibroblast growth factor-19
KeywordsHORMONE/GROWTH FACTOR / BETA TREFOIL / DISULPHIDE BONDS / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / neural crest cell migration / bile acid and bile salt transport / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway ...negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / neural crest cell migration / bile acid and bile salt transport / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling / neurogenesis / regulation of cell migration / positive regulation of D-glucose import across plasma membrane / positive regulation of JNK cascade / response to bacterium / growth factor activity / Negative regulation of FGFR4 signaling / positive regulation of protein phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / nervous system development / PIP3 activates AKT signaling / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / response to ethanol / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Fibroblast growth factor 15/19/21 / 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 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHarmer, N.J. / Pellegrini, L. / Chirgadze, D. / Fernandez-Recio, J. / Blundell, T.L.
CitationJournal: Biochemistry / Year: 2004
Title: The crystal structure of fibroblast growth factor (FGF) 19 reveals novel features of the FGF family and offers a structural basis for its unusual receptor affinity.
Authors: Harmer, N.J. / Pellegrini, L. / Chirgadze, D. / Fernandez-Recio, J. / Blundell, T.L.
History
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Aug 16, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4274
Polymers18,1171
Non-polymers3103
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.573, 67.573, 193.374
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

21A-304-

HOH

31A-362-

HOH

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Components

#1: Protein Fibroblast growth factor-19 / FGF-19


Mass: 18116.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF19 / Plasmid: pGAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: O95750
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, potassium phosphate, magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMTris-HCl1drop
2200 mM1dropNaCl
312-14 %(w/w)PEG33501reservoir
40.25 M1reservoirMgSO4
50.1 Mpotassium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2003 / Details: mirrors
RadiationMonochromator: Rh coated silica / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. all: 42313 / % possible obs: 99.9 % / Redundancy: 12.08 % / Biso Wilson estimate: 13.695 Å2 / Rsym value: 0.062 / Net I/σ(I): 36.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 4.32 / Num. unique all: 2080 / Rsym value: 0.586 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 23.33 Å / Num. obs: 42303 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 4.33

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1JQZ, 2FGF, 1IJT, 1QQK, 1IHK

1jqz

2fgf

1ijt

1qqk

1ihk


Resolution: 1.3→23.33 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 0.508 / SU ML: 0.022 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 2058 -RANDOM
Rwork0.1798 ---
all0.1807 ---
obs0.1807 42303 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.373 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.046 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.3→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 19 267 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211032
X-RAY DIFFRACTIONr_bond_other_d0.0040.02958
X-RAY DIFFRACTIONr_angle_refined_deg1.4372.0031395
X-RAY DIFFRACTIONr_angle_other_deg1.0532243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245121
X-RAY DIFFRACTIONr_chiral_restr0.0990.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021093
X-RAY DIFFRACTIONr_gen_planes_other0.010.02196
X-RAY DIFFRACTIONr_nbd_refined0.230.2174
X-RAY DIFFRACTIONr_nbd_other0.2780.21172
X-RAY DIFFRACTIONr_nbtor_other0.0840.2598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2660.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.245
X-RAY DIFFRACTIONr_mcbond_it1.2441.5629
X-RAY DIFFRACTIONr_mcangle_it1.9721024
X-RAY DIFFRACTIONr_scbond_it2.2583403
X-RAY DIFFRACTIONr_scangle_it3.554.5371
X-RAY DIFFRACTIONr_rigid_bond_restr1.29121032
X-RAY DIFFRACTIONr_sphericity_free4.1082267
X-RAY DIFFRACTIONr_sphericity_bonded2.95421012
LS refinement shellResolution: 1.298→1.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 148 -
Rwork0.19 3054 -
obs-2906 100 %
Refinement
*PLUS
Highest resolution: 1.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.44

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