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- PDB-1se7: Solution structure of the E. coli bacteriophage P1 encoded HOT pr... -

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Entry
Database: PDB / ID: 1se7
TitleSolution structure of the E. coli bacteriophage P1 encoded HOT protein: a homologue of the theta subunit of E. coli DNA polymerase III
ComponentsHOMOLOGUE OF THE THETA SUBUNIT OF DNA POLYMERASE III
KeywordsTRANSFERASE / E. COLI BACTERIOPHAGE P1 / HOMOLOGUE OF THETA / HOT / E. COLI DNA POLYMERASE III
Function / homology
Function and homology information


DNA replication / DNA-directed DNA polymerase activity / DNA binding
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
Biological speciesEnterobacteria phage P1 (virus)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsDeRose, E.F. / Kirby, T.W. / Mueller, G.A. / Chikova, A.K. / Schaaper, R.M. / London, R.E.
CitationJournal: Structure / Year: 2004
Title: Phage Like It HOT: Solution Structure of the Bacteriophage P1-Encoded HOT Protein, a Homolog of the theta Subunit of E. coli DNA Polymerase III
Authors: Derose, E.F. / Kirby, T.W. / Mueller, G.A. / Chikova, A.K. / Schaaper, R.M. / London, R.E.
History
DepositionFeb 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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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Assembly

Deposited unit
A: HOMOLOGUE OF THE THETA SUBUNIT OF DNA POLYMERASE III


Theoretical massNumber of molelcules
Total (without water)9,7101
Polymers9,7101
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)7 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HOMOLOGUE OF THE THETA SUBUNIT OF DNA POLYMERASE III / HOT


Mass: 9709.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: HOT / Plasmid: pET30HOT / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: Q71T70

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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
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.3mM U-[13C,15N] protein, 5mM Tris, 100mM NaCl, 5mM NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
NMRPipe2.1 Rev 2002.044.17.08processing
NMRView5.0.4data analysis
ARIA1.2structure solution
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The structures were computed using default ARIA parameters, with qrelax set to false. 430 manually assigned NOE distance restraints were included, and qshift and qexclude were set to false ...Details: The structures were computed using default ARIA parameters, with qrelax set to false. 430 manually assigned NOE distance restraints were included, and qshift and qexclude were set to false for the manually assigned NOEs. ARIA assigned 1140 unambiguous and 435 ambiguous NOE distance restraints. 51 dihedral restraints, 46 hydrogen bond restraints, and 36 backbone amide residual dipolar couplings were also used in the calculation.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 7

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