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- PDB-5woz: NMR solution structure of Rtt103 (RTT) protein using two 4D-spectra -

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Basic information

Entry
Database: PDB / ID: 5woz
TitleNMR solution structure of Rtt103 (RTT) protein using two 4D-spectra
ComponentsRegulator of Ty1 transposition protein 103
KeywordsTRANSCRIPTION REGULATOR / RNA polymerase II core binder
Function / homology
Function and homology information


RNA polymerase II C-terminal domain phosphoserine binding / retrotransposon silencing / mRNA 3'-end processing / RNA polymerase II transcribes snRNA genes / RNA polymerase II complex binding / site of double-strand break / chromatin / DNA binding / nucleus
Similarity search - Function
: / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Regulator of Ty1 transposition protein 103
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / na
AuthorsEvangelidis, T. / Nerli, S. / Sgourakis, N.G. / Tripsianes, K.
CitationJournal: Nat Commun / Year: 2018
Title: Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.
Authors: Evangelidis, T. / Nerli, S. / Novacek, J. / Brereton, A.E. / Karplus, P.A. / Dotas, R.R. / Venditti, V. / Sgourakis, N.G. / Tripsianes, K.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 103


Theoretical massNumber of molelcules
Total (without water)16,1331
Polymers16,1331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7940 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Regulator of Ty1 transposition protein 103


Mass: 16132.574 Da / Num. of mol.: 1 / Fragment: residues 5-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RTT103, YDR289C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05543

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D HC(CC TOCSY(CO))NH
121isotropic14D 13C,15N edited HMQC-NOESY-HSQC
131isotropic14D 13C,13C edited HMQC-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-13C; U-15N] Rtt103 (RTT) protein, 95% H2O/5% D2O
Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.8 mM / Component: Rtt103 (RTT) protein / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 35 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
4D-CHAINSEvangelidis and Tripsianeschemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxdata analysis
SparkyGoddardpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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