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- PDB-2k7r: N-terminal domain of the Bacillus subtilis helicase-loading prote... -

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Basic information

Entry
Database: PDB / ID: 2k7r
TitleN-terminal domain of the Bacillus subtilis helicase-loading protein DnaI
ComponentsPrimosomal protein dnaI
KeywordsREPLICATION / DnaI N-terminal domain / helicase-loading protein / ATP-binding / DNA replication / Nucleotide-binding / Primosome
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Primosomal DnaI, N-terminal / Primosomal protein DnaI N-terminus / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative helicase loader DnaI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsThe helicase loader protein DnaI (the Bacillus subtilis homologue of Escherichia coli DnaC) is ...The helicase loader protein DnaI (the Bacillus subtilis homologue of Escherichia coli DnaC) is required to load the hexameric helicase DnaC (the B. subtilis homologue of E. coli DnaB) onto DNA at the start of replication
AuthorsLoscha, K.V. / Jaudzems, K. / Ioannou, C. / Su, X.C. / Hill, F.R. / Otting, G. / Dixon, N.E. / Liepinsh, E.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader
Authors: Loscha, K.V. / Jaudzems, K. / Ioannou, C. / Su, X.C. / Hill, F.R. / Otting, G. / Dixon, N.E. / Liepinsh, E.
History
DepositionAug 19, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 dnaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6092
Polymers12,5431
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Primosomal protein dnaI


Mass: 12543.268 Da / Num. of mol.: 1 / Fragment: UNP residues 1-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dnaI, ytxA, BSU28980 / Production host: Escherichia coli (E. coli) / References: UniProt: P06567
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The helicase loader protein DnaI (the Bacillus subtilis homologue of Escherichia coli DnaC) is required to load the hexameric helicase DnaC (the B. subtilis homologue of E. coli DnaB) onto ...Details: The helicase loader protein DnaI (the Bacillus subtilis homologue of Escherichia coli DnaC) is required to load the hexameric helicase DnaC (the B. subtilis homologue of E. coli DnaB) onto DNA at the start of replication
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D HNHA
1312D 1H-1H NOESY
1412D DQF-COSY
1512D 1H-1H TOCSY
1612D 1H-15N HSQC
1712D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.5mM [U-95% 15N] DnaI, 0.5mM zinc ion, 10% [U-99% 2H] D2O, 90% H2O, 10mM sodium phosphate, 0.1% sodium azide, 100mM sodium chloride, 1mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDnaI[U-95% 15N]1
0.5 mMZINC ION1
10 %D2O[U-99% 2H]1
90 %H2O1
10 mMsodium phosphate1
0.1 %sodium azide1
100 mMsodium chloride1
1 mMDTT1
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges, Readrefinement
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
MOLMOLKoradi, Billeter, Wuthrichdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss, Thodata analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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