BMRB Entry 16986

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16986
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Title:
N-terminal domain of the DP1 subunit of an archaeal D-family DNA polymerase
Deposition date:
2010-06-09
Original release date:
2010-07-26
Authors:
Yamasaki, Kazuhiko; Matsui, Ikuo
Citation:

Citation: Yamasaki, Kazuhiko; Urushibata, Yuji; Yamasaki, Tomoko; Arisaka, Fumio; Matsui, Ikuo. "Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases."  FEBS Lett. 584, 3370-3375 (2010).
PubMed: 20598295

Assembly members:

Assembly members:
entity, polymer, 75 residues, 8252.611 Da.

Natural source:

Natural source:   Common Name: Pyrococcus horikoshii   Taxonomy ID: 53953   Superkingdom: Archaea   Kingdom: not available   Genus/species: Pyrococcus horikoshii

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSHMDEFVKGLMKNGYLITP SAYYLLVGHFNEGKFSLIEL IKFAKSRETFIIDDEIANEF LKSIGAEVELPQEIK

Data sets:
Data typeCount
13C chemical shifts183
15N chemical shifts72
1H chemical shifts537

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DP1 subunit1

Entities:

Entity 1, DP1 subunit 75 residues - 8252.611 Da.

1   GLYSERHISMETASPGLUPHEVALLYSGLY
2   LEUMETLYSASNGLYTYRLEUILETHRPRO
3   SERALATYRTYRLEULEUVALGLYHISPHE
4   ASNGLUGLYLYSPHESERLEUILEGLULEU
5   ILELYSPHEALALYSSERARGGLUTHRPHE
6   ILEILEASPASPGLUILEALAASNGLUPHE
7   LEULYSSERILEGLYALAGLUVALGLULEU
8   PROGLNGLUILELYS

Samples:

sample_1: sodium phosphate 150 mM; H2O 95%; D2O 5%; DP1 subunit, [U-99% 15N], 0.7 – 3.3 mM

sample_2: sodium phosphate 150 mM; D2O 100%; DP1 subunit, [U-99% 13C; U-99% 15N], 0.7 – 3.3 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 5.5; pressure: 1 atm; temperature: 318 K

sample_conditions_2: ionic strength: 0.15 M; pH: 5.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HMQC-NOESY-HMQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_2

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

  • Bruker DMX 750 MHz
  • Bruker DMX 500 MHz

Related Database Links:

PDB
DBJ BAA29192
REF WP_010884237
SP O57863
AlphaFold O57863

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks