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- PDB-1lr7: Crystal structure of Fs1, the heparin-binding domain of follistat... -

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Basic information

Entry
Database: PDB / ID: 1lr7
TitleCrystal structure of Fs1, the heparin-binding domain of follistatin, complexed with the heparin analogue sucrose octasulphate (SOS)
Componentsfollistatin
Keywordshormone/growth factor / heparin-binding / cystine-rich / sucrose octasulphate / 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 / hair follicle morphogenesis / negative regulation of epithelial cell differentiation / female gonad development / odontogenesis of dentin-containing tooth / keratinocyte proliferation / BMP signaling pathway / hematopoietic progenitor cell differentiation / skeletal system development / cellular response to growth factor stimulus / cell differentiation / nucleolus / 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 superfamily / TGF-beta binding (TB) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain ...Follistatin, N-terminal / : / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / 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 / MAD / Resolution: 1.5 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 1.3Dec 21, 2022Group: 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 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 600 heterogen Authors claimed that there was a lack of connecting electron density between sulphate ... heterogen Authors claimed that there was a lack of connecting electron density between sulphate groups in the ligand sucrose octasulphate due to possible alternative binding modes. Accordingly, the authors chose to list the sulphate ions as free ions even though they belong to the sucrose octasulphate molecule.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: follistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8236
Polymers8,3431
Non-polymers4805
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.593, 38.153, 78.497
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


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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30-35% 2-propanol, 0.6-0.7 M ammonium acetate, 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-IDDetails
115 mg/mlprotein1drop
230-35 %2-propanol1reservoir
30.6-0.7 Mammonium acetate1reservoir
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: 1.5→39.2 Å / Num. obs: 10456 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.21 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.196 / % possible all: 71.8
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 71.8 % / Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→39.22 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.873 / SU ML: 0.07 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22211 499 4.8 %RANDOM
Rwork0.18892 ---
all0.1905 10412 --
obs0.1905 9913 94.87 %-
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: 15.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--1.77 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 30 78 630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021559
X-RAY DIFFRACTIONr_bond_other_d0.0010.02464
X-RAY DIFFRACTIONr_angle_refined_deg2.0992.037762
X-RAY DIFFRACTIONr_angle_other_deg0.88631084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.944372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.5761590
X-RAY DIFFRACTIONr_chiral_restr0.1180.279
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02602
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0292
X-RAY DIFFRACTIONr_nbd_refined0.260.3109
X-RAY DIFFRACTIONr_nbd_other0.20.3436
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.562
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2390.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0650.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2891.5364
X-RAY DIFFRACTIONr_mcangle_it2.0732577
X-RAY DIFFRACTIONr_scbond_it3.2273195
X-RAY DIFFRACTIONr_scangle_it4.8624.5185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 19 -
Rwork0.181 556 -
obs-556 72.15 %
Refinement
*PLUS
Lowest resolution: 39.2 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.94

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