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- PDB-7wcg: Single-Stranded DNA binding protein of Sulfolobus Solfataricus st... -

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Basic information

Entry
Database: PDB / ID: 7wcg
TitleSingle-Stranded DNA binding protein of Sulfolobus Solfataricus structure at high-temperature
ComponentsSingle-stranded DNA binding protein Ssb
KeywordsDNA BINDING PROTEIN / OB-fold / Hyperthermophilic / Structure at high-temperature
Function / homology: / Single-stranded DNA binding protein Ssb-like, OB fold / response to ionizing radiation / double-strand break repair via homologous recombination / chromosome / Nucleic acid-binding, OB-fold / DNA binding / cytoplasm / Single-stranded DNA binding protein Ssb
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYang, M.J. / Park, C. / Lee, W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2022
Title: NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus .
Authors: Yang, M.J. / Kim, J. / Lee, Y. / Lee, W. / Park, C.J.
History
DepositionDec 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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: Single-stranded DNA binding protein Ssb


Theoretical massNumber of molelcules
Total (without water)14,1631
Polymers14,1631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Single-stranded DNA binding protein Ssb / SSB


Mass: 14162.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Strain: P2 / Gene: ssb / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97W73

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
182isotropic12D 1H-13C HSQC
122isotropic13D HNCO
132isotropic13D HN(CA)CO
142isotropic13D CBCA(CO)NH
162isotropic13D HN(CA)CB
172isotropic13D C(CO)NH
1102isotropic13D HBHA(CO)NH
192isotropic13D H(CCO)NH
151isotropic13D 1H-15N NOESY
1112isotropic23D 1H-13C NOESY aliphatic
1121isotropic13D 1H-15N TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM [U-15N] Single-stranded binding protein of Sulfolobus Solfataricus with C-term His-tag, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution2500 uM [U-13C; U-15N] Single-stranded binding protein of Sulfolobus Solfataricus with C-term His-tag, 90% H2O/10% D2O15N, 13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMSingle-stranded binding protein of Sulfolobus Solfataricus with C-term His-tag[U-15N]1
500 uMSingle-stranded binding protein of Sulfolobus Solfataricus with C-term His-tag[U-13C; U-15N]2
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PONDEROSA-C/SLee, Stark, and Markleystructure calculation
AUDANALee, Petit, Cornilescu, Stark, and Markleystructure calculation
NMRFAM-SPARKYLee, Tonelli, and Markleychemical shift assignment
PINE-SPARKYLee, Westler, Bahrami, Eghbalnia, and Markleychemical shift assignment
NMRFAM-SPARKYLee, Tonelli, and Markleypeak picking
APESShin, Lee, and Leepeak picking
PONDEROSA-C/SLee, Stark, and Markleyrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 8
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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