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- PDB-5unk: NMR structure of the RED subdomain of the Sleeping Beauty transposase -

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Basic information

Entry
Database: PDB / ID: 5unk
TitleNMR structure of the RED subdomain of the Sleeping Beauty transposase
ComponentsSleeping Beauty transposase
KeywordsDNA BINDING PROTEIN / helical / helix-turn-helix / dna-binding / transposase
Function / homologyTransposase, Tc1-like / Transposase / DNA transposition / Homeobox-like domain superfamily / DNA integration / Winged helix-like DNA-binding domain superfamily / DNA binding / HTH_Tnp_Tc3_2 domain-containing protein
Function and homology information
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodSOLUTION NMR
AuthorsKonnova, T.A. / Singer, C.M. / Nesmelova, I.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM112076 United States
CitationJournal: Protein Sci. / Year: 2017
Title: NMR solution structure of the RED subdomain of the Sleeping Beauty transposase.
Authors: Konnova, T.A. / Singer, C.M. / Nesmelova, I.V.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sleeping Beauty transposase


Theoretical massNumber of molelcules
Total (without water)7,1221
Polymers7,1221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5540 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -
RepresentativeModel #1medoid

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Components

#1: Protein Sleeping Beauty transposase


Mass: 7122.414 Da / Num. of mol.: 1 / Fragment: UNP residues 50-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / Gene: GSONMT00020475001 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060ZAA1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D CBCA(CO)NH
132isotropic13D (H)CCH-TOCSY
141isotropic13D 1H-15N TOCSY
151isotropic13D 1H-15N NOESY
162isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mg/mL [U-13C; U-15N] RED subdomain of the Sleeping Beauty transposase, 20 mM MES, 650 mM sodium sulfate, 95% H2O/5% D2O15N, 13C95% H2O/5% D2O
solution22 mg/mL [U-13C; U-15N] RED subdomain of the Sleeping Beauty transposase, 20 mM MES, 650 mM sodium sulfate, 100% D2O15N, 13C100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLRED subdomain of the Sleeping Beauty transposase[U-13C; U-15N]1
20 mMMESnatural abundance1
650 mMsodium sulfatenatural abundance1
2 mg/mLRED subdomain of the Sleeping Beauty transposase[U-13C; U-15N]2
20 mMMESnatural abundance2
650 mMsodium sulfatenatural abundance2
Sample conditionsIonic strength: 650 mM / Label: solution / pH: 5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 950 MHz

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Processing

NMR software
NameDeveloperClassification
xplor-nihSchwieters, C. D., Kuszewski, J. J., Tjandra, N. and Clore, G. M. (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson. 160, 65-73structure calculation
CARAKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpinBruker Biospincollection
NMR representativeSelection criteria: medoid
NMR ensembleConformers submitted total number: 10

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