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- PDB-2aya: Solution Structure of the C-Terminal 14 kDa Domain of the tau sub... -

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Basic information

Entry
Database: PDB / ID: 2aya
TitleSolution Structure of the C-Terminal 14 kDa Domain of the tau subunit from Escherichia coli DNA Polymerase III
ComponentsDNA polymerase III subunit tau
KeywordsTRANSFERASE / KH-fold / c-terminus of polymerase III tau subunit
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / DNA clamp loader activity / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...DNA polymerase III, clamp loader complex / DNA clamp loader activity / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNA polymerase III, tau subunit, domain V / DNA polymerase III, tau subunit, domain V / DNA polymerase III subunit tau, DnaB-binding domain IV / DNA polymerase III, tau subunit, domain V superfamily / DNA polymerase III, subunit gamma/tau, helical lid domain / DNA polymerase III subunits tau domain IV DnaB-binding / DNA polymerase III tau subunit V interacting with alpha / DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III ...DNA polymerase III, tau subunit, domain V / DNA polymerase III, tau subunit, domain V / DNA polymerase III subunit tau, DnaB-binding domain IV / DNA polymerase III, tau subunit, domain V superfamily / DNA polymerase III, subunit gamma/tau, helical lid domain / DNA polymerase III subunits tau domain IV DnaB-binding / DNA polymerase III tau subunit V interacting with alpha / DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / DNA polymerase III, delta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / ClpA/B family / 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
DNA polymerase III subunit tau
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJergic, S. / Dixon, N.E. / Otting, G. / Su, X.C.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit.
Authors: Su, X.C. / Jergic, S. / Keniry, M.A. / Dixon, N.E. / Otting, G.
History
DepositionSep 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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 subunit tau


Theoretical massNumber of molelcules
Total (without water)14,3521
Polymers14,3521
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 / 200The submitted conformer models are the 20 structures with the lowest energy violations
RepresentativeModel #1the structure closest to the average

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Components

#1: Protein DNA polymerase III subunit tau


Mass: 14352.188 Da / Num. of mol.: 1 / Fragment: tau subunit of DNA polymerase III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaX, dnaZ, dnaZX / Plasmid: pSJ1308 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06710, 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
121HN(CA)CB
131CACB(CO)NH
141HNCO
151HNCA
161HN(CO)CA
171HNHA
1813D 13C-separated NOESY
19213C-HSQC
11032D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM tau14 15N,13C; 5 mM phosphate buffer with 100 mM NaCl; pH 6.8; 90% H2O, 10% D2O90% H2O/10% D2O
20.6 mM tau14 10% 13C; 5 mM phosphate buffer with 100 mM NaCl; pH 6.8; 90% H2O, 10% D2O90% H2O/10% D2O
31.8 mM tau14, 5 mM phosphate buffer with 100 mM NaCl; pH 6.8; 90% H2O, 10% D2O90% H2O/10% D2O
41.8 mM tau14, 5 mM phosphate buffer with 100 mM NaCl; pD 7.0; 100% D2O100% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.8 / Pressure: 1 atm / Temperature: 303 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 INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Brukerprocessing
DYANA1.5Guentertstructure solution
PROSA6.1Guentertprocessing
OPAL2.6Luginbuehlrefinement
CARA1.2Dambergerdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1891 NOE-derived distance constraints and 241 dihedral angle restraints.
NMR representativeSelection criteria: the structure closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest energy violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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