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- PDB-1jqr: NMR structure of the African swine fever virus DNA polymerase X -

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Basic information

Entry
Database: PDB / ID: 1jqr
TitleNMR structure of the African swine fever virus DNA polymerase X
ComponentsDNA POLYMERASE BETA-LIKE
KeywordsVIRAL PROTEIN / DNA Polymerase
Function / homology
Function and homology information


virion component / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding
Similarity search - Function
Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily ...Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsByeon, I.-J.L. / Su, M.-I. / Showalter, A.K. / Tsai, M.-D.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Solution structure of a viral DNA polymerase X and evidence for a mutagenic function.
Authors: Showalter, A.K. / Byeon, I.J. / Su, M.I. / Tsai, M.D.
History
DepositionAug 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE BETA-LIKE


Theoretical massNumber of molelcules
Total (without water)20,3511
Polymers20,3511
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)21 / 80structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein DNA POLYMERASE BETA-LIKE / DNA Polymerase X


Mass: 20351.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Genus: Asfivirus / Gene: O174L / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P42494

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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
1323D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM or 1 mM protein U-15N,13C; 50 mM borate, 50 mM KCl, 1 mM DTT, 1 mM EDTA95% H2O/5% D2O
21 mM protein U-15N,13C; 50 mM borate, 50 mM KCl, 1 mM DTT, 1 mM EDTA100% D2O
3unlabeled 0.5 mM protein; 50 mM borate, 50 mM KCl, 1 mM DTT, 1 mM EDTA95% H2O/5% D2O
4unlabeled 0.5 mM protein; 50 mM borate, 50 mM KCl, 1 mM DTT, 1 mM EDTA100% D2O
Sample conditionsIonic strength: 50 mM borate, 50 mM KCl, 1 mM DTT, 1 mM EDTA
pH: 7.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERcollection
XwinNMR2.6BRUKERprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2597 restraints, 2241 are NOE-derived distance restraints, 244 TALOS-derived dihedral angle restraints, and 112 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 21

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