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- PDB-6xor: Structure of the Self-Association Domain of Swallow -

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Basic information

Entry
Database: PDB / ID: 6xor
TitleStructure of the Self-Association Domain of Swallow
ComponentsProtein swallow
KeywordsRNA BINDING PROTEIN / coiled coil / self-association domain
Function / homology
Function and homology information


pole plasm mRNA localization / bicoid mRNA localization / regulation of pole plasm oskar mRNA localization / anterior/posterior axis specification, embryo / dynein complex binding / actin filament organization / cell cycle / cell division / mRNA binding / nucleus
Similarity search - Function
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsLoening, N.M. / Barbar, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1617019 United States
National Science Foundation (NSF, United States)1617019 Amendment No. 1 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Structural characterization of the self-association domain of swallow.
Authors: Loening, N.M. / Barbar, E.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: 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 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein swallow
B: Protein swallow


Theoretical massNumber of molelcules
Total (without water)17,1192
Polymers17,1192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3750 Å2
ΔGint-32 kcal/mol
Surface area10790 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein swallow


Mass: 8559.464 Da / Num. of mol.: 2 / Mutation: R224E, K244I, C253D, C265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: swa, CG3429 / Plasmid: Champion pET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40688

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-13C NOESY
152isotropic33D 1H-13C NOESY aromatic
162isotropic33D 1H-13C NOESY
171isotropic13D HN(CA)CB
181isotropic33D HN(COCA)CB
1161isotropic13D HN(CA)CO
1151isotropic23D HNCO
1141isotropic23D C(CO)NH
1131isotropic23D H(CCO)NH
1121isotropic43D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.5 mM [U-99% 13C; U-99% 15N] Residues 205-275 of Swallow, 10 mM sodium chloride, 20 mM MES, 1 mM sodium azide, 0.2 mM DSS, 95% H2O/5% D2O13C,15N_sample95% H2O/5% D2O
solution20.4 mM [U-99% 13C; U-99% 15N] Residues 205-275 of Swallow, 10 mM sodium chloride, 20 mM MES, 1 mM sodium azide, 0.2 mM DSS, 0.4 mM unlabeled Residues 205-275 of Swallow, 95% H2O/5% D2O13C,15N_mixed_sample95% H2O/5% D2O50% 13C/15N labeled protein, 50% unlabeled protein
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMResidues 205-275 of Swallow[U-99% 13C; U-99% 15N]1
10 mMsodium chloridenatural abundance1
20 mMMESnatural abundance1
1 mMsodium azidenatural abundance1
0.2 mMDSSnatural abundance1
0.4 mMResidues 205-275 of Swallow[U-99% 13C; U-99% 15N]2
10 mMsodium chloridenatural abundance2
20 mMMESnatural abundance2
1 mMsodium azidenatural abundance2
0.2 mMDSSnatural abundance2
0.4 mMunlabeled Residues 205-275 of Swallownatural abundance2
Sample conditionsIonic strength: 30 mM / Label: conditions_1 / pH: 5.6 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIBrukerAVANCE II6002
Bruker AVANCE IIIBrukerAVANCE III9003
Bruker AVANCE IIIBrukerAVANCE III7004
Bruker AVANCE III HDBrukerAVANCE III HD8005

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.5CCPNchemical shift assignment
CcpNmr Analysis2.5CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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