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- PDB-1du2: SOLUTION STRUCTURE OF THE THETA SUBUNIT OF DNA POLYMERASE III -

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Basic information

Entry
Database: PDB / ID: 1du2
TitleSOLUTION STRUCTURE OF THE THETA SUBUNIT OF DNA POLYMERASE III
ComponentsDNA POLYMERASE III
KeywordsTRANSFERASE / DNA polymerase / Alpha Helix
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 / torsion angle dynamics
AuthorsKeniry, M.A. / Berthon, H.A. / Yang, J.-Y. / Miles, C.S. / Dixon, N.E.
CitationJournal: Protein Sci. / Year: 2000
Title: NMR solution structure of the theta subunit of DNA polymerase III from Escherichia coli.
Authors: Keniry, M.A. / Berthon, H.A. / Yang, J.Y. / Miles, C.S. / Dixon, N.E.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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


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)20 / 400target function
RepresentativeModel #1fewest violations

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Components

#1: Protein DNA POLYMERASE III


Mass: 8861.305 Da / Num. of mol.: 1 / Fragment: THETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCM869 / 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 15N-separated NOESY
1213D 15N-separated TOCSY
131HNHA
141HNHB
2523D 13C-separated NOESY
3632D NOESY
NMR detailsText: The structure was determined by double and triple resonance heteronuclear NMR spectroscopy techniques. There is evidence of substantial conformational exchange in sections of the chain that ...Text: The structure was determined by double and triple resonance heteronuclear NMR spectroscopy techniques. There is evidence of substantial conformational exchange in sections of the chain that severely limit the precision of the structure in these regions of the molecule. Specifically, conformational exchange occurs in the regions D19-M33 and L55-S63.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Theta subunit U-15N; 10 mM phosphate buffer pH 6.5;90% H2O/10% D2O
21 mM Theta subunit U-15N,13C; 10 mM phosphate buffer, pH 6.590% H2O/10% D2O
31 mM Theta subunit; 10 mM phosphate buffer pH 6.5;100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.036.5aambient 298 K
20.036.5ambient 298 K
30.036.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian VXRSVarianVXRS5002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2 and 6.1Varian Associatescollection
XEASY1.3.10Bartelsdata analysis
SPSCAN1.0.53Glaserrefinement
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on 819 restraints, 511 are NOE-derived distance constraints, 300 dihedral angle restraints and 8 distance restraints from hydrogen bonds
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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