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- PDB-2axd: solution structure of the theta subunit of escherichia coli DNA p... -

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Basic information

Entry
Database: PDB / ID: 2axd
Titlesolution structure of the theta subunit of escherichia coli DNA polymerase III in complex with the epsilon subunit
ComponentsDNA polymerase III, theta subunit
KeywordsTRANSFERASE / THETA SUBUNIT / DNA POLYMERASE III
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. / Park, A.Y. / Owen, E.A. / Hamdan, S.M. / Pintacuda, G. / Otting, G. / Dixon, N.E.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit
Authors: Keniry, M.A. / Park, A.Y. / Owen, E.A. / Hamdan, S.M. / Pintacuda, G. / Otting, G. / Dixon, N.E.
History
DepositionSep 5, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: DNA polymerase III, theta subunit


Theoretical massNumber of molelcules
Total (without water)8,8611
Polymers8,8611
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 200structures 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 / Plasmid: PCM869 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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
1223D 15N-separated NOESY
1313D 13C-separated NOESY
1423D 13C-separated NOESY
151HNHA
1622D 15N-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING DISTANCE AND ANGULAR RESTRAINTS AND SUPPLEMENTED WITH RESTRAINTS CALCULATED FROM PSEUDO-CONTACT SHIFTS INDUCED BY INSERTING A LANTHANIDE ION INTO THE EPSILON186 BINDING POCKET

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Sample preparation

Details
Solution-IDContentsSolvent system
11MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM PHOSPHATE BUFFER Na; 90% H20, 10% D2O90% H20, 10% D2O
21MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM TRIS BUFFER; 90% H20, 10% D2O90% H20, 10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1VARIAN ASSOCIATEScollection
XEASY1.4C.BARTELS, T.XIA, M.BILLETER, P.GUENTERT, K.WUETHRICHdata analysis
Sparky3.11T.GODDARD, D.KNELLERdata analysis
DYANA1.5P.GUENTERTrefinement
XPLOR-NIH2.9.7C.SCHWIETERS, N.TJANDRA, J.KUSZEWSKI, G.CLORErefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 632 DISTANCE RESTRAINTS, 111 DIHEDRAL ANGLE RESTRAINTS AND 162 PSEUDO-CONTACT SHIFT RESTRAINTS. THE PSEUDO-CONTACT SHIFTS WERE CALCULATED FROM THE CHANGE IN ...Details: THE STRUCTURES ARE BASED ON 632 DISTANCE RESTRAINTS, 111 DIHEDRAL ANGLE RESTRAINTS AND 162 PSEUDO-CONTACT SHIFT RESTRAINTS. THE PSEUDO-CONTACT SHIFTS WERE CALCULATED FROM THE CHANGE IN CHEMICAL SHIFT OF THE AMIDE PROTONS INDUCED BY INSERTING A LANTHANIDE ION (EITHER YSPROSIUM, ERBIUM OR HOLMIUM) AT THE METAL BINDING SITE OF EPSILON-186 WHICH IS COMPLEXED TO THE THETA SUBUNIT. XPLOR-NIH 2.9.7 WAS USED TO REFINE THE STRUCTURE USING THIS DATA
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 12

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