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- PDB-2ru8: DnaT C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2ru8
TitleDnaT C-terminal domain
ComponentsPrimosomal protein 1
KeywordsREPLICATION / Primosome / replication restart / DnaT / DNA binding
Function / homology
Function and homology information


DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / replication fork processing / protein homotrimerization / DNA-templated DNA replication / single-stranded DNA binding / magnesium ion binding / identical protein binding
Similarity search - Function
Primosomal protein 1 / DnaT, DNA-binding domain / DnaT DNA-binding domain
Similarity search - Domain/homology
Primosomal protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsAbe, Y. / Tani, J. / Fujiyama, S. / Urabe, M. / Sato, K. / Aramaki, T. / Katayama, T. / Ueda, T.
CitationJournal: Febs J. / Year: 2014
Title: Structure and mechanism of the primosome protein DnaT-functional structures for homotrimerization, dissociation of ssDNA from the PriB·ssDNA complex, and formation of the DnaT·ssDNA complex.
Authors: Fujiyama, S. / Abe, Y. / Tani, J. / Urabe, M. / Sato, K. / Aramaki, T. / Katayama, T. / Ueda, T.
History
DepositionJan 29, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: Primosomal protein 1


Theoretical massNumber of molelcules
Total (without water)11,2381
Polymers11,2381
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Primosomal protein 1 / DnaT


Mass: 11237.618 Da / Num. of mol.: 1 / Fragment: ssDNA binding domain, UNP residues 89-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8J2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HN(CO)CA
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11413D 1H-15N NOESY
11513D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] DnaT-1, 20 mM HEPES-2, 90% H2O/10% D2O90% H2O/10% D2O
20.1 mM [U-99% 15N] DnaT-3, 20 mM HEPES-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDnaT-1[U-99% 13C; U-99% 15N]1
20 mMHEPES-21
0.1 mMDnaT-3[U-99% 15N]2
20 mMHEPES-42
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxprediction of torsion angle
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
Oliviaolivia developer teamchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 752 / NOE intraresidue total count: 251 / NOE long range total count: 101 / NOE medium range total count: 157 / NOE sequential total count: 243 / Hydrogen bond constraints total count: 26 / Protein phi angle constraints total count: 55 / Protein psi angle constraints total count: 55
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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