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- PDB-1jaj: Solution Structure of DNA Polymerase X from the African Swine Fev... -

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Basic information

Entry
Database: PDB / ID: 1jaj
TitleSolution Structure of DNA Polymerase X from the African Swine Fever Virus
ComponentsDNA POLYMERASE BETA-LIKE PROTEIN
KeywordsVIRAL PROTEIN / Cis peptide
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 / torsion angle dynamics energy minimization
AuthorsMaciejewski, M.W. / Shin, R. / Pan, B. / Mullen, G.P.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Solution structure of a viral DNA repair polymerase.
Authors: Maciejewski, M.W. / Shin, R. / Pan, B. / Marintchev, A. / Denninger, A.
#1: Journal: J.BIOMOL.NMR / Year: 2001
Title: 1H, 15N, and 13C Resonance Assignments for a 20 kDa DNA Polymerase from African Swine Fever Virus
Authors: Maciejewski, M.W. / Pan, B. / Shin, R. / Denninger, A. / Mullen, G.P.
History
DepositionMay 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Feb 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_software / pdbx_validate_close_contact / pdbx_validate_torsion / struct_mon_prot_cis
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.conformer_id / _pdbx_nmr_software.name / _pdbx_validate_close_contact.PDB_model_num / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_mon_prot_cis.pdbx_omega_angle
Revision 2.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE BETA-LIKE PROTEIN


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)25 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA POLYMERASE BETA-LIKE PROTEIN


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 / Strain: BA71V / Gene: O174L / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42494

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D 13C-separated NOESY
3233D 15N-separated NOESY
333HNHA
4442D NOESY
NMR detailsText: Talos was used in conjunction with backbone resonance assignments to generate angle constraints.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM DNA Polymerase X U-15N,13C; 500 mM NaCl; 20 mM PIPES (pH 6.5); 10 mM DTT; 0.5 mM AEBSF; 0.02% sodium azide90% H2O/10% D2O
21.0 mM DNA Polymerase X U-15N,13C; 500 mM NaCl; 20 mM PIPES (pH 6.5); 10 mM DTT; 0.5 mM AEBSF; 0.02% sodium azide100% D2O
31.0 mM DNA Polymerase X U-15N; 500 mM NaCl; 20 mM PIPES (pH 6.5); 10 mM DTT; 0.5 mM AEBSF; 0.02% sodium azide90% H2O/10% D2O
41.0 mM DNA Polymerase X; 500 mM NaCl; 20 mM PIPES (pH 6.5); 10 mM DTT; 0.5 mM AEBSF; 0.02% sodium azide100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1500 mM 6.5ambient 298 K
2500 mM 6.5ambient 298 K
3500 mM 6.5ambient 298 K
4500 mM 6.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian, Inc.collection
NMRPipe1.8Delaglioprocessing
XEASY1.13Bartlesdata analysis
DYANA1.5Guentertstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics energy minimization / Software ordinal: 1
Details: 200 random strucutres were calculated within Dyana. The 50 with the lowest target function were refined in xplor with energy minimization and the 25 with the lowest energy in xplor were selected for deposition.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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