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- PDB-2e0g: DnaA N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2e0g
TitleDnaA N-terminal domain
ComponentsChromosomal replication initiator protein dnaA
KeywordsREPLICATION / domain structure / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


DnaA-oriC complex / DnaA-DiaA complex / DnaA-Dps complex / DnaA-HU complex / replication inhibiting complex / regulation of DNA-templated DNA replication initiation / positive regulation of DNA-templated DNA replication initiation / regulation of DNA replication / DNA unwinding involved in DNA replication / DNA replication origin binding ...DnaA-oriC complex / DnaA-DiaA complex / DnaA-Dps complex / DnaA-HU complex / replication inhibiting complex / regulation of DNA-templated DNA replication initiation / positive regulation of DNA-templated DNA replication initiation / regulation of DNA replication / DNA unwinding involved in DNA replication / DNA replication origin binding / DNA replication initiation / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / cytoplasmic side of plasma membrane / DNA replication / sequence-specific DNA binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
DnaA, N-terminal domain / DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain ...DnaA, N-terminal domain / DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator / GMP Synthetase; Chain A, domain 3 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAbe, Y. / Katayama, T. / Ueda, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure and Function of DnaA N-Terminal Domains: Specific Sites and Mechanisms in Inter-DnaA Interaction and in DnaB Helicase Loading on oriC
Authors: Abe, Y. / Jo, T. / Matsuda, Y. / Matsunaga, C. / Katayama, T. / Ueda, T.
History
DepositionOct 7, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
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

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Assembly

Deposited unit
A: Chromosomal replication initiator protein dnaA


Theoretical massNumber of molelcules
Total (without water)11,9241
Polymers11,9241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Chromosomal replication initiator protein dnaA


Mass: 11924.439 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: dnaA / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03004

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM DnaA N-terminal domain U-15N, 13C, 50mM phospate buffer (pH6.5), 20mM EDTA, 40mM KCl, 2mM DTT, 10% sucrose; 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM DnaA N-terminal domain U-13C, 50mM phospate buffer (pH6.5), 20mM EDTA, 40mM KCl, 2mM DTT, 10% sucrose; 100% D2O100% D2O
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.refinement
CYANA2.1structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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