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- PDB-2ae9: Solution Structure of the theta subunit of DNA polymerase III fro... -

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Basic information

Entry
Database: PDB / ID: 2ae9
TitleSolution Structure of the theta subunit of DNA polymerase III from E. coli
ComponentsDNA polymerase III, theta subunit
KeywordsTRANSFERASE / all helical / 3 helices
Function / homology
Function and homology information


DNA polymerase III, core complex / DNA polymerase III complex / lagging strand elongation / replisome / leading strand elongation / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / cytosol
Similarity search - Function
DNA polymerase III-theta / DNA polymerase III-theta, bacterial / DNA polymerase III-theta superfamily / DNA polymerase III, theta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase III subunit theta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, G.A. / Kirby, T.W. / Derose, E.F. / Li, D. / Schaaper, R.M. / London, R.E.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Nuclear Magnetic Resonance Solution Structure of the Escherichia coli DNA Polymerase III {theta} Subunit.
Authors: Mueller, G.A. / Kirby, T.W. / Derose, E.F. / Li, D. / Schaaper, R.M. / London, R.E.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III, theta subunit


Theoretical massNumber of molelcules
Total (without water)8,8611
Polymers8,8611
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA polymerase III, theta subunit


Mass: 8861.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: holE / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABS8, DNA-directed DNA polymerase

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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
2323D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM theta U-15N,13C; 10 mM NaPi pH 6.5 10 M EDTA, 5mM NaN354 % H2O; 6 % D2O; 40% d3- Methanol
2600 uM theta U-15N,13C; 10 mM NaPi pH 6.5 10 M EDTA, 5mM NaN360% D2O; 40% d4- Methanol
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1.CVariancollection
NMRPipe2005Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CNS1.1Brungerrefinement
ARIA1.2Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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