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- PDB-2kxe: N-terminal domain of the DP1 subunit of an archaeal D-family DNA ... -

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Basic information

Entry
Database: PDB / ID: 2kxe
TitleN-terminal domain of the DP1 subunit of an archaeal D-family DNA polymerase
ComponentsDNA polymerase II small subunit
KeywordsTRANSFERASE / DNA polymerase / D-family / small subunit / archara / helical bundle
Function / homology
Function and homology information


: / : / exodeoxyribonuclease I / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
D-family DNA polymerase, DP1 subunit N-terminal domain / DNA polymerase II small subunit, archaeal / DNA polymerase delta/II small subunit family / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase II small subunit
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYamasaki, K. / Matsui, I.
CitationJournal: Febs Lett. / Year: 2010
Title: Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases
Authors: Yamasaki, K. / Urushibata, Y. / Yamasaki, T. / Arisaka, F. / Matsui, I.
History
DepositionApr 30, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DNA polymerase II small subunit


Theoretical massNumber of molelcules
Total (without water)8,5351
Polymers8,5351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA polymerase II small subunit / / DP1 subunit / Pol II


Mass: 8534.804 Da / Num. of mol.: 1 / Fragment: residues 1-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O57863, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCA
1713D HN(CO)CA
1813D (H)CCH-COSY
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D 1H-13C NOESY
11313D HMQC-NOESY-HMQC
11412D 1H-15N HSQC
21522D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-3.3mM sodium phosphate; 0.7-3.3mM [U-99% 15N] sodium phosphate; 0.7-3.3mM [U-99% 13C; U-99% 15N] sodium phosphate; 95% H2O/5% D2O95% H2O/5% D2O
23.3mM [U-99% 15N] sodium phosphate; 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMsodium phosphate-10.7-3.31
mMsodium phosphate-2[U-99% 15N]0.7-3.31
mMsodium phosphate-3[U-99% 13C; U-99% 15N]0.7-3.31
3.3 mMsodium phosphate-4[U-99% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.15 5.5 ambient 318 K
20.15 5.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionClassification
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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