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- PDB-2haj: Solution structure of the helicase-binding domain of Escherichia ... -

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Basic information

Entry
Database: PDB / ID: 2haj
TitleSolution structure of the helicase-binding domain of Escherichia coli primase
ComponentsDNA primase
KeywordsTRANSFERASE / DNA polymerase / helicase / primase / helix
Function / homology
Function and homology information


DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / replisome / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA binding ...DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / replisome / replication fork processing / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal ...DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA Primase, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / Toprim-like / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSu, X.C. / Loscha, K.V. / Dixon, N.E. / Otting, G.
CitationJournal: Febs J. / Year: 2006
Title: Monomeric solution structure of the helicase-binding domain of Escherichia coli DnaG primase
Authors: Su, X.C. / Schaeffer, P.M. / Loscha, K.V. / Gan, P.H.P. / Dixon, N.E. / Otting, G.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / 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 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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

Downloads & links

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Assembly

Deposited unit
A: DNA primase


Theoretical massNumber of molelcules
Total (without water)16,7191
Polymers16,7191
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 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA primase


Mass: 16718.969 Da / Num. of mol.: 1 / Fragment: Helicase-binding domain, residues 447-581
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaG / Plasmid: pKL1176 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0ABS5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131(H)CCH-TOCSY
141CC(CO)NH
1522D NOESY
1622D TOCSY
172DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3mM DnaG-C U-15N, 13C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
20.3mM DnaG-C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.10 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, P.structure solution
TopSpin1.3Brukerprocessing
CARA1.2Kellerdata analysis
Sparky1.5Goddarddata analysis
CYANA2Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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