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- PDB-2p23: Crystal structure of human FGF19 -

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Basic information

Entry
Database: PDB / ID: 2p23
TitleCrystal structure of human FGF19
ComponentsFibroblast growth factor 19
KeywordsSIGNALING PROTEIN / atypical beta-trefoil fold
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 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling ...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 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling / regulation of cell migration / positive regulation of glucose import / Negative regulation of FGFR4 signaling / animal organ morphogenesis / positive regulation of JNK cascade / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / 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: 1.8 Å
AuthorsMohammadi, M.
CitationJournal: Mol.Cell.Biol. / Year: 2007
Title: Molecular insights into the klotho-dependent, endocrine mode of action of fibroblast growth factor 19 subfamily members.
Authors: Goetz, R. / Beenken, A. / Ibrahimi, O.A. / Kalinina, J. / Olsen, S.K. / Eliseenkova, A.V. / Xu, C. / Neubert, T.A. / Zhang, F. / Linhardt, R.J. / Yu, X. / White, K.E. / Inagaki, T. / ...Authors: Goetz, R. / Beenken, A. / Ibrahimi, O.A. / Kalinina, J. / Olsen, S.K. / Eliseenkova, A.V. / Xu, C. / Neubert, T.A. / Zhang, F. / Linhardt, R.J. / Yu, X. / White, K.E. / Inagaki, T. / Kliewer, S.A. / Yamamoto, M. / Kurosu, H. / Ogawa, Y. / Kuro-O, M. / Lanske, B. / Razzaque, M.S. / Mohammadi, M.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 19
B: Fibroblast growth factor 19


Theoretical massNumber of molelcules
Total (without water)43,4272
Polymers43,4272
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.297, 67.297, 54.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 21713.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLys-S / References: UniProt: O95750
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 100 mM tri-sodium citrate, 14% PEG 1000, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 2005
RadiationMonochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 25585 / Num. obs: 25585 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.05 / Net I/σ(I): 25.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4 % / Num. unique all: 2564 / Rsym value: 0.34 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PWA

1pwa


Resolution: 1.8→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2491 -Random
Rwork0.251 ---
all-25259 --
obs-25259 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.441 Å2-0.277 Å20 Å2
2--2.441 Å20 Å2
3----4.882 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 48 2140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005985
X-RAY DIFFRACTIONc_angle_d1.30172
X-RAY DIFFRACTIONc_improper_angle_d0.93492

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