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- PDB-5td6: C. elegans FOG-3 BTG/Tob domain - H47N, C117A -

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Basic information

Entry
Database: PDB / ID: 5td6
TitleC. elegans FOG-3 BTG/Tob domain - H47N, C117A
ComponentsFOG-3 protein
KeywordsRNA BINDING PROTEIN / BTG/Tob / polymer / RNA binding
Function / homology
Function and homology information


masculinization of hermaphroditic germ-line / positive regulation of oocyte development / cell fate specification / nuclear periphery / transcription corepressor activity / spermatogenesis / regulation of gene expression / nucleus / cytoplasm
Similarity search - Function
Tob1/2 / Anti-proliferative protein / BTG-like domain superfamily / BTG family / tob/btg1 family
Similarity search - Domain/homology
Anti_prolifrtn domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.034 Å
AuthorsAoki, S.T. / Bingman, C.A. / Wickens, M. / Kimble, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5K99HD081208 United States
CitationJournal: Cell Rep / Year: 2018
Title: An RNA-Binding Multimer Specifies Nematode Sperm Fate.
Authors: Aoki, S.T. / Porter, D.F. / Prasad, A. / Wickens, M. / Bingman, C.A. / Kimble, J.
History
DepositionSep 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FOG-3 protein
B: FOG-3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5293
Polymers32,4332
Non-polymers961
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.992, 64.992, 133.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
SymmetryHelical symmetry: (Num. of operations: 1 / Rise per n subunits: 32.461 Å / Rotation per n subunits: 180 °)

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Components

#1: Protein FOG-3 protein / Feminization Of Germline


Mass: 16216.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-137 / Mutation: H47N, C117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: N2 / Gene: fog-3, C03C11.2, CELE_C03C11.2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): Rosetta2 / References: UniProt: G5EDX7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: Mg Acetate, Na Citrate, PEG 10000 / PH range: 5.4-5.8
Temp details: set trays up at RT, moved to cold room (4 Celsius)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.034→29.22 Å / Num. obs: 21617 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.0498 / Rsym value: 0.05399 / Net I/σ(I): 24.12
Reflection shellResolution: 2.034→2.106 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7383 / Mean I/σ(I) obs: 2.56 / CC1/2: 0.789 / % possible all: 98.18

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D5R

2d5r


Resolution: 2.034→29.22 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 21.9
Details: Author claims "Two densities were observed in the solvent-accessible area adjacent to residues 52-56 in both copies in the ASU. Density is observed at FoFc contour levels past 6 sigma. We ...Details: Author claims "Two densities were observed in the solvent-accessible area adjacent to residues 52-56 in both copies in the ASU. Density is observed at FoFc contour levels past 6 sigma. We attempted modeling of acetate (too small) and citrate (too large), both present in the crystallization conditions, but the fit was unsatisfactory. Thus, the final uploaded model does not account for these two large densities."
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1993 9.22 %random
Rwork0.1769 ---
obs0.1816 21616 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.034→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 5 138 2195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092128
X-RAY DIFFRACTIONf_angle_d1.1032902
X-RAY DIFFRACTIONf_dihedral_angle_d13.523772
X-RAY DIFFRACTIONf_chiral_restr0.046322
X-RAY DIFFRACTIONf_plane_restr0.006378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0335-2.08440.28671350.22841323X-RAY DIFFRACTION97
2.0844-2.14070.28291400.21221352X-RAY DIFFRACTION100
2.1407-2.20370.27271430.21281388X-RAY DIFFRACTION100
2.2037-2.27480.26091400.21051390X-RAY DIFFRACTION100
2.2748-2.35610.2391370.19041397X-RAY DIFFRACTION100
2.3561-2.45040.25031400.18741379X-RAY DIFFRACTION100
2.4504-2.56180.25721420.21407X-RAY DIFFRACTION100
2.5618-2.69680.2871410.21461392X-RAY DIFFRACTION100
2.6968-2.86560.26151430.20581396X-RAY DIFFRACTION100
2.8656-3.08660.28171430.21171396X-RAY DIFFRACTION100
3.0866-3.39690.24791410.19411402X-RAY DIFFRACTION100
3.3969-3.88740.1941500.15981433X-RAY DIFFRACTION100
3.8874-4.8940.18021420.13321446X-RAY DIFFRACTION100
4.894-29.22350.20641560.16211522X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.5469 Å / Origin y: 51.3325 Å / Origin z: 63.2053 Å
111213212223313233
T0.2422 Å2-0.0492 Å2-0.0057 Å2-0.1918 Å20.0161 Å2--0.2061 Å2
L1.3251 °2-0.2928 °20.2704 °2-1.9135 °2-0.5216 °2--0.9225 °2
S0.1017 Å °-0.0783 Å °-0.1029 Å °0.0077 Å °-0.1035 Å °-0.0028 Å °0.0055 Å °0.0089 Å °0 Å °
Refinement TLS groupSelection details: all

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