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- PDB-6urs: Sleeping Beauty transposase PAI subdomain mutant - H19Y -

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Basic information

Entry
Database: PDB / ID: 6urs
TitleSleeping Beauty transposase PAI subdomain mutant - H19Y
ComponentsSleeping Beauty transposase PAI subdomain
KeywordsDNA BINDING PROTEIN / transposase
Function / homologyBromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily / chromatin binding / BAH domain-containing protein
Function and homology information
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodSOLUTION NMR / na
AuthorsNesmelova, I.V. / Leighton, G.O. / Yan, C. / Lustig, J. / Corona, R.I. / Guo, J.T. / Ivics, Z.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM128100 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM112076 United States
National Science Foundation (NSF, United States)DBI0844749 United States
National Science Foundation (NSF, United States)DBI1356459 United States
CitationJournal: To Be Published
Title: H19Y mutation in the primary DNA-recognition subdomain of the Sleeping Beauty transposase improves structural stability, transposon DNA-binding and transposition
Authors: Nesmelova, I.V. / Leighton, G.O. / Yan, C. / Lustig, J. / Corona, R.I. / Guo, J.T. / Ivics, Z.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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: Sleeping Beauty transposase PAI subdomain


Theoretical massNumber of molelcules
Total (without water)6,3891
Polymers6,3891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 100structures with the least restraint violations
RepresentativeModel #1medoid

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Components

#1: Protein Sleeping Beauty transposase PAI subdomain


Mass: 6389.402 Da / Num. of mol.: 1 / Mutation: H19Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / Gene: GSONMT00045019001 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060XYS9*PLUS

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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
131isotropic13D 1H-15N TOCSY
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY
261isotropic22D 1H-15N HSQC
281isotropic13D HN(CA)CB
271isotropic13D CBCA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] pai subdomain mutant, 90% H2O/10% D2O
Details: 25 mM sodium phosphate buffer / Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: pai subdomain mutant / Isotopic labeling: [U-13C; U-15N]
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
125 mM sodium phosphate buffer25 mMconditions_15 1 atm278 K
225 mM sodium phosphate buffer DNA TCGGAAGTTTACATACAC25 mMconditions_25 1 atm308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: na / Software ordinal: 2
Details: after water refinemnet in X-PLOR NIH, the structures were further refined to improve side-chain geometry
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 8

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