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- PDB-1lr9: STRUCTURE OF Fs1, THE HEPARIN-BINDING DOMAIN OF FOLLISTATIN -

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Basic information

Entry
Database: PDB / ID: 1lr9
TitleSTRUCTURE OF Fs1, THE HEPARIN-BINDING DOMAIN OF FOLLISTATIN
ComponentsFollistatin
KeywordsHORMONE/GROWTH FACTOR / follistatin / heparin-binding / Fs1 / cystine-rich / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Antagonism of Activin by Follistatin / activin receptor antagonist activity / negative regulation of follicle-stimulating hormone secretion / ameloblast differentiation / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / pattern specification process / activin binding / negative regulation of activin receptor signaling pathway ...Antagonism of Activin by Follistatin / activin receptor antagonist activity / negative regulation of follicle-stimulating hormone secretion / ameloblast differentiation / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / pattern specification process / activin binding / negative regulation of activin receptor signaling pathway / heparan sulfate proteoglycan binding / negative regulation of epithelial cell differentiation / hair follicle morphogenesis / female gonad development / odontogenesis of dentin-containing tooth / keratinocyte proliferation / BMP signaling pathway / hematopoietic progenitor cell differentiation / skeletal system development / response to organic cyclic compound / cellular response to growth factor stimulus / cell differentiation / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / cytoplasm
Similarity search - Function
Follistatin, N-terminal / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 ...Follistatin, N-terminal / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsInnis, C.A. / Hyvonen, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structures of the Heparan Sulfate-binding Domain of Follistatin: Insights into ligand binding.
Authors: Innis, C.A. / Hyvonen, M.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Dec 21, 2022Group: 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 1.5Sep 20, 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: Follistatin


Theoretical massNumber of molelcules
Total (without water)8,3431
Polymers8,3431
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.551, 43.733, 77.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Follistatin / FS1 / Activin-binding protein


Mass: 8342.812 Da / Num. of mol.: 1 / Fragment: Heparin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21674
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.35 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30-35% PEG4000, 0.4 M Magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
230-35 %PEG40001reservoir
30.4 M1reservoirMgCl2
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2001 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→38.6 Å / Num. obs: 2787 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 33.26 Å2 / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.171 / % possible all: 90.4
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 38.6 Å / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 90.4 % / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LR7

1lr7


Resolution: 2.5→38.63 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.856 / SU B: 12.462 / SU ML: 0.287 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.65 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 126 4.6 %RANDOM
Rwork0.21972 ---
all0.22151 2766 --
obs0.22151 2766 98.26 %-
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: 24.605 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2--2.76 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 0 28 555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021540
X-RAY DIFFRACTIONr_bond_other_d0.0010.02469
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.991732
X-RAY DIFFRACTIONr_angle_other_deg0.98931096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.791372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.4081593
X-RAY DIFFRACTIONr_chiral_restr0.0940.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02607
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0296
X-RAY DIFFRACTIONr_nbd_refined0.210.3128
X-RAY DIFFRACTIONr_nbd_other0.2140.3458
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4950.535
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2220.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.33
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.315
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.5364
X-RAY DIFFRACTIONr_mcangle_it1.6862575
X-RAY DIFFRACTIONr_scbond_it2.8053176
X-RAY DIFFRACTIONr_scangle_it4.7594.5157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 7 -
Rwork0.213 172 -
obs-172 86.5 %
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 38.6 Å / Num. reflection obs: 2639 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65

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