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- PDB-6maa: WFIKKN2 Follistatin Domain -

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Basic information

Entry
Database: PDB / ID: 6maa
TitleWFIKKN2 Follistatin Domain
ComponentsWAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2
KeywordsPEPTIDE BINDING PROTEIN / WFIKKN2 / GASP / Kazal / Follsitatin
Function / homology
Function and homology information


receptor antagonist activity / metalloendopeptidase inhibitor activity / muscle cell development / transforming growth factor beta binding / roof of mouth development / negative regulation of DNA binding / transforming growth factor beta receptor signaling pathway / negative regulation of protein binding / skeletal system development / negative regulation of transforming growth factor beta receptor signaling pathway ...receptor antagonist activity / metalloendopeptidase inhibitor activity / muscle cell development / transforming growth factor beta binding / roof of mouth development / negative regulation of DNA binding / transforming growth factor beta receptor signaling pathway / negative regulation of protein binding / skeletal system development / negative regulation of transforming growth factor beta receptor signaling pathway / serine-type endopeptidase inhibitor activity / extracellular space / extracellular region
Similarity search - Function
WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1/2 / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Kazal domain superfamily / Kazal domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module ...WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1/2 / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Kazal domain superfamily / Kazal domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Kazal domain profile. / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
NITRATE ION / WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.394 Å
AuthorsMcCoy, J.C. / Walker, R.G. / Thomas, T.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM114640 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structure of the WFIKKN2 follistatin domain reveals insight into how it inhibits growth differentiation factor 8 (GDF8) and GDF11.
Authors: McCoy, J.C. / Walker, R.G. / Murray, N.H. / Thompson, T.B.
History
DepositionAug 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3225
Polymers10,0741
Non-polymers2484
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.460, 46.460, 95.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

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Components

#1: Protein WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2 / Growth and differentiation factor-associated serum protein 1 / mGASP-1


Mass: 10074.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wfikkn2, Gasp1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): Rosetta / References: UniProt: Q7TQN3
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe "LVPRGS" is a thrombin cleavage site

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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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: ammonium Nitrate, sodium citrate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→41.8 Å / Num. all: 277020 / Num. obs: 21677 / % possible obs: 99.7 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Net I/σ(I): 25.5
Reflection shellResolution: 1.39→1.42 Å / Rmerge(I) obs: 0.166 / Num. measured obs: 10502 / Rpim(I) all: 0.08

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Processing

Software
NameVersionClassification
PHENIXdev_2450refinement
PDB_EXTRACT3.24data extraction
MOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.394→23.23 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.42
RfactorNum. reflection% reflection
Rfree0.1801 1035 4.79 %
Rwork0.1645 --
obs0.1653 21597 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.58 Å2 / Biso mean: 17.9174 Å2 / Biso min: 6.47 Å2
Refinement stepCycle: final / Resolution: 1.394→23.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms598 0 16 156 770
Biso mean--25.6 32.26 -
Num. residues----78
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004627
X-RAY DIFFRACTIONf_angle_d0.745843
X-RAY DIFFRACTIONf_chiral_restr0.0787
X-RAY DIFFRACTIONf_plane_restr0.004111
X-RAY DIFFRACTIONf_dihedral_angle_d20.802239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.394-1.46750.18911340.119728793013100
1.4675-1.55940.15211580.112428833041100
1.5594-1.67980.12661380.117529103048100
1.6798-1.84880.18441470.132929123059100
1.8488-2.11610.1691550.143429453100100
2.1161-2.66550.19941550.169729723127100
2.6655-23.23320.18861480.2043061320997

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