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- PDB-2ntd: Human fibroblast growth factor-1 (140 amino acid form) with Cys11... -

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Basic information

Entry
Database: PDB / ID: 2ntd
TitleHuman fibroblast growth factor-1 (140 amino acid form) with Cys117Val/Pro134Cys mutations
ComponentsAcidic fibroblast growth factor 1
KeywordsHORMONE/GROWTH FACTOR / beta-trefoil / HORMONE-GROWTH FACTOR COMPLEX
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 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / 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 / activation of protein kinase B activity / 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 cell division / positive regulation of intracellular signal transduction / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / 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 / Signaling by FGFR2 in disease / neurogenesis / Signaling by FGFR1 in disease / positive regulation of endothelial cell migration / lung development / regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / growth factor activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / wound healing / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / positive regulation of cholesterol biosynthetic process / integrin binding / extracellular matrix / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of angiogenesis / 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
FORMIC ACID / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsDubey, V.K. / Blaber, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Spackling the Crack: Stabilizing Human Fibroblast Growth Factor-1 by Targeting the N and C terminus beta-Strand Interactions
Authors: Dubey, V.K. / Lee, J. / Somasundaram, T. / Blaber, S. / Blaber, M.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acidic fibroblast growth factor 1
B: Acidic fibroblast growth factor 1
C: Acidic fibroblast growth factor 1
D: Acidic fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,26115
Polymers66,7554
Non-polymers50611
Water5,531307
1
A: Acidic fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8274
Polymers16,6891
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acidic fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8274
Polymers16,6891
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acidic fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8274
Polymers16,6891
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acidic fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7813
Polymers16,6891
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.600, 108.330, 60.920
Angle α, β, γ (deg.)90.00, 104.97, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer. There are four monomers in the ASU (chain identifiers A, B, C, and D).

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Components

#1: Protein
Acidic fibroblast growth factor 1 / Heparin-binding growth factor 1 / HBGF-1 / aFGF / Beta-endothelial cell growth factor / ECGF- beta


Mass: 16688.764 Da / Num. of mol.: 4 / Mutation: C117V, P134C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli (E. coli) / References: UniProt: P05230
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.6M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 22, 2005
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20.14 Å / Num. all: 25332 / Num. obs: 25003 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.96 / Num. unique all: 1591 / % possible all: 95.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JY0

1jy0


Resolution: 2.52→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 221276.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 991 4.8 %RANDOM
Rwork0.173 ---
obs0.173 20565 79.6 %-
all-25332 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.3724 Å2 / ksol: 0.356448 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20.98 Å2
2---4.23 Å20 Å2
3---1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.52→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 0 340 4934
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2.52→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 103 5.1 %
Rwork0.21 1923 -
obs--46.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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