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- PDB-2mna: The structural basis of DNA binding by the single-stranded DNA-bi... -

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Basic information

Entry
Database: PDB / ID: 2mna
TitleThe structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus
Components
  • Single-stranded DNA binding protein (SSB)
  • ssDNA
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / SSB / Sulfolobus solfataricus / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


response to ionizing radiation / double-strand break repair via homologous recombination / chromosome / DNA binding / cytoplasm
Similarity search - Function
: / Single-stranded DNA binding protein Ssb-like, OB fold / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / Single-stranded DNA binding protein Ssb
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsGamsjaeger, R. / Kariawasam, R. / Gimenez, A.X. / Touma, C.F. / McIlwain, E. / Bernardo, R.E. / Shepherd, N.E. / Ataide, S.F. / Dong, A.Q. / Richard, D.J. ...Gamsjaeger, R. / Kariawasam, R. / Gimenez, A.X. / Touma, C.F. / McIlwain, E. / Bernardo, R.E. / Shepherd, N.E. / Ataide, S.F. / Dong, A.Q. / Richard, D.J. / White, M.F. / Cubeddu, L.
CitationJournal: Biochem.J. / Year: 2015
Title: The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus
Authors: Gamsjaeger, R. / Kariawasam, R. / Gimenez, A.X. / Touma, C. / McIlwain, E. / Bernardo, R.E. / Shepherd, N.E. / Ataide, S.F. / Dong, Q. / Richard, D.J. / White, M.F. / Cubeddu, L.
History
DepositionApr 2, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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
B: ssDNA
A: Single-stranded DNA binding protein (SSB)


Theoretical massNumber of molelcules
Total (without water)14,5602
Polymers14,5602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain ssDNA


Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Single-stranded DNA binding protein (SSB)


Mass: 12779.369 Da / Num. of mol.: 1 / Fragment: UNP residues 1-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSB, SSO2364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W73

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
2212D 1H-13C HSQC
2313D HCC(CO)NH-TOCSY
2413D (H)CCH-TOCSY
2512D 15N13C filtered NOESY
2613D 1H-15N NOESY
2713D 1H-13C NOESY aliphatic
2813D 1H-13C NOESY aromatic
2913D 15N13C filtered (F1) NOESY aliphatic
21013D 15N13C filtered (F1) NOESY aromatic
11112D 1H-15N HSQC
11212D 1H-13C HSQC
11313D CBCA(CO)NH
11413D HNCO
11513D HN(CA)CB
11613D HCC(CO)NH-TOCSY
11713D CC(CO)NH-TOCSY
11813D HN(CA)CO
11913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.8-1.5 mM [U-100% 13C; U-100% 15N] SsoSSB-1, 90 % H2O-2, 10 % D2O-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSsoSSB-1[U-100% 13C; U-100% 15N]0.8-1.51
90 %H2O-21
10 %D2O-31

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameClassification
ARIArefinement
HADDOCKrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, torsion angle dynamics, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10 / Representative conformer: 1

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