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- PDB-1qqk: THE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 7 (KERATINOCYTE... -

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Basic information

Entry
Database: PDB / ID: 1qqk
TitleTHE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 7 (KERATINOCYTE GROWTH FACTOR)
ComponentsFIBROBLAST GROWTH FACTOR 7
KeywordsHORMONE/GROWTH FACTOR / BETA-TREFOIL / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


secretion by lung epithelial cell involved in lung growth / FGFR2b ligand binding and activation / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / type 2 fibroblast growth factor receptor binding / PI-3K cascade:FGFR2 / PI3K Cascade / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / positive regulation of keratinocyte proliferation ...secretion by lung epithelial cell involved in lung growth / FGFR2b ligand binding and activation / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / type 2 fibroblast growth factor receptor binding / PI-3K cascade:FGFR2 / PI3K Cascade / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / positive regulation of keratinocyte proliferation / Negative regulation of FGFR2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of epithelial cell proliferation involved in lung morphogenesis / positive regulation of myoblast proliferation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / phosphatidylcholine biosynthetic process / positive regulation of keratinocyte migration / mesenchymal cell proliferation / phospholipid biosynthetic process / branching involved in salivary gland morphogenesis / regulation of synapse maturation / surfactant homeostasis / endothelial cell proliferation / protein localization to cell surface / RAF/MAP kinase cascade / myoblast proliferation / hair follicle morphogenesis / positive chemotaxis / chemoattractant activity / positive regulation of cell division / fibroblast growth factor receptor signaling pathway / ovarian follicle development / neurogenesis / positive regulation of endothelial cell proliferation / regulation of cell migration / positive regulation of epithelial cell proliferation / epithelial cell proliferation / GABA-ergic synapse / growth factor activity / lung development / heparin binding / actin cytoskeleton organization / postsynapse / positive regulation of MAPK cascade / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / Golgi apparatus / extracellular space / extracellular region / 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
Fibroblast growth factor 7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsYe, S. / Luo, Y. / Pelletier, H. / McKeehan, W.L.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural basis for interaction of FGF-1, FGF-2, and FGF-7 with different heparan sulfate motifs.
Authors: Ye, S. / Luo, Y. / Lu, W. / Jones, R.B. / Linhardt, R.J. / Capila, I. / Toida, T. / Kan, M. / Pelletier, H. / McKeehan, W.L.
#1: Journal: Biochemistry / Year: 1998
Title: The glycine box: a determinant of specificity for fibroblast growth factor
Authors: Luo, Y. / Lu, W. / Mohamedali, K.A. / Jang, J.H. / Jones, R.B. / Gabriel, J.L. / Kan, M. / McKeehan, W.L.
#2: Journal: Science / Year: 1989
Title: Human KGF is FGF-related with properties of a paracrine effector of epithelial cell growth.
Authors: Finch, P.W. / Rubin, J.S. / Miki, T. / Ron, D. / Aaronson, S.A.
#3: Journal: Nature / Year: 1998
Title: Structure of a heparin-linked biologically active dimer of fibroblast growth factor.
Authors: DiGabriele, A.D. / Lax, I. / Chen, D.I. / Svahn, C.M. / Jaye, M. / Schlessinger, J. / Hendrickson, W.A.
#4: Journal: Science / Year: 1996
Title: Heparin structure and interactions with basic fibroblast growth factor.
Authors: Faham, S. / Hileman, R.E. / Fromm, J.R. / Linhardt, R.J. / Rees, D.C.
History
DepositionJun 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 7
B: FIBROBLAST GROWTH FACTOR 7


Theoretical massNumber of molelcules
Total (without water)32,5402
Polymers32,5402
Non-polymers00
Water2,306128
1
A: FIBROBLAST GROWTH FACTOR 7


Theoretical massNumber of molelcules
Total (without water)16,2701
Polymers16,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FIBROBLAST GROWTH FACTOR 7


Theoretical massNumber of molelcules
Total (without water)16,2701
Polymers16,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.1, 169.1, 62.6
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein FIBROBLAST GROWTH FACTOR 7


Mass: 16269.858 Da / Num. of mol.: 2 / Fragment: FGF-7BETA (SER-54)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: PROSTATE / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02195
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: SODIUM PHOSPHATE, POTASSIUM PHOSPHATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMHEPES1droppH7.0
32.56 Msodium potassium phosphate1reservoirpH5.0
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9296
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9296 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 8036 / Num. obs: 8036 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 12.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.447 / % possible all: 81.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 48247
Reflection shell
*PLUS
% possible obs: 81.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.1→10 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.324 702 -RANDOM
Rwork0.233 ---
all0.261 7381 --
obs0.242 6920 84 %-
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 0 128 2157
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.131
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS

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