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- PDB-6jza: Structure of Fstl1 -

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Basic information

Entry
Database: PDB / ID: 6jza
TitleStructure of Fstl1
ComponentsFollistatin-related protein 1
KeywordsANTITUMOR PROTEIN / TGF / development / signaling / dimer
Function / homology
Function and homology information


Signaling by BMP / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / hematopoietic stem cell homeostasis / regulation of BMP signaling pathway / endothelial cell differentiation / endothelial cell migration / heparin binding / cell differentiation / calcium ion binding ...Signaling by BMP / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / hematopoietic stem cell homeostasis / regulation of BMP signaling pathway / endothelial cell differentiation / endothelial cell migration / heparin binding / cell differentiation / calcium ion binding / negative regulation of apoptotic process / extracellular space / extracellular region
Similarity search - Function
: / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / 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 ...: / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / 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 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Follistatin-related protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsLiu, X. / Ning, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870730 China
CitationJournal: Protein Sci. / Year: 2019
Title: Structural and functional study of FK domain of Fstl1.
Authors: Li, X. / Li, L. / Chang, Y. / Ning, W. / Liu, X.
History
DepositionApr 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Follistatin-related protein 1


Theoretical massNumber of molelcules
Total (without water)9,0111
Polymers9,0111
Non-polymers00
Water61334
1
A: Follistatin-related protein 1

A: Follistatin-related protein 1


Theoretical massNumber of molelcules
Total (without water)18,0232
Polymers18,0232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area2860 Å2
ΔGint-13 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.731, 45.731, 68.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-128-

HOH

21A-129-

HOH

31A-132-

HOH

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Components

#1: Protein Follistatin-related protein 1 / Follistatin-like protein 1 / TGF-beta-inducible protein TSC-36


Mass: 9011.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fstl1, Frp, Fstl, Tsc36 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62356
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 1.2 M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 3669 / % possible obs: 99.89 % / Redundancy: 9.95 % / Net I/σ(I): 25.3
Reflection shellResolution: 2.3→2.37 Å / Num. unique obs: 465 / % possible all: 99.98

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→26.007 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 33.12
RfactorNum. reflection% reflection
Rfree0.2357 159 4.33 %
Rwork0.202 --
obs0.2036 3669 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.57 Å2 / Biso mean: 35.12 Å2 / Biso min: 23.68 Å2
Refinement stepCycle: final / Resolution: 2.3→26.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms618 0 0 34 652
Biso mean---40.77 -
Num. residues----81
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01636
X-RAY DIFFRACTIONf_angle_d1.253848
X-RAY DIFFRACTIONf_chiral_restr0.08389
X-RAY DIFFRACTIONf_plane_restr0.005111
X-RAY DIFFRACTIONf_dihedral_angle_d16.845240
LS refinement shellResolution: 2.3003→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2357 159 -
Rwork0.202 3510 -
all-3669 -
obs--100 %

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