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- PDB-1q1u: Crystal structure of human FHF1b (FGF12b) -

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Basic information

Entry
Database: PDB / ID: 1q1u
TitleCrystal structure of human FHF1b (FGF12b)
Componentsfibroblast growth factor homologous factor 1
KeywordsHORMONE/GROWTH FACTOR / FGF-12 / Human / crystal structure / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


regulation of voltage-gated sodium channel activity / regulation of neuronal action potential / positive regulation of sodium ion transport / regulation of sodium ion transmembrane transport / cardiac muscle cell action potential involved in contraction / neuromuscular process / Phase 0 - rapid depolarisation / sodium channel regulator activity / JNK cascade / neurogenesis ...regulation of voltage-gated sodium channel activity / regulation of neuronal action potential / positive regulation of sodium ion transport / regulation of sodium ion transmembrane transport / cardiac muscle cell action potential involved in contraction / neuromuscular process / Phase 0 - rapid depolarisation / sodium channel regulator activity / JNK cascade / neurogenesis / adult locomotory behavior / growth factor activity / cell-cell signaling / nervous system development / heparin binding / heart development / chemical synaptic transmission / transmembrane transporter binding / synapse / signal transduction / extracellular space / nucleus / 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 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOlsen, S.K. / Garbi, M. / Zampieri, N. / Eliseenkova, A.V. / Ornitz, D.M. / Goldfarb, M. / Mohammadi, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Fibroblast growth factor (FGF) homologous factors share structural but not functional homology with FGFs
Authors: Olsen, S.K. / Garbi, M. / Zampieri, N. / Eliseenkova, A.V. / Ornitz, D.M. / Goldfarb, M. / Mohammadi, M.
History
DepositionJul 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Aug 16, 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

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Assembly

Deposited unit
A: fibroblast growth factor homologous factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7505
Polymers16,3661
Non-polymers3844
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.624, 58.853, 65.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein fibroblast growth factor homologous factor 1 / FGF-12 / FGF12b / fibroblast growth factor 12 isoform 2 / myocyte-activating factor / Fgf12 protein


Mass: 16365.646 Da / Num. of mol.: 1 / Fragment: residues 1-144 / Mutation: C144A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: T7 promoter driven expression / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61328
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 31.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 400, 200mM ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
145 mg/mlprotein1drop
225 mMHEPES1droppH7.5
3300 mM1dropNaCl
420-25 %PEG4001reservoir
5200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.920218
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2002
RadiationMonochromator: Kohzu double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920218 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 13559 / Num. obs: 13171 / % possible obs: 97 % / Observed criterion σ(I): 0 / Rsym value: 0.058 / Net I/σ(I): 7.03
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 85 % / % possible all: 85
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 93909 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Rmerge(I) obs: 0.365

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1IHK

1ihk


Resolution: 1.7→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1307 10.3 %random
Rwork0.223 ---
all0.2231 12734 --
obs0.2231 12734 --
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 20 36 1142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.31
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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