BMRB Entry 15926

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15926
MolProbity Validation Chart

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Title:
N-terminal domain of the Bacillus subtilis helicase-loading protein DnaI
Deposition date:
2008-08-19
Original release date:
2009-04-04
Authors:
Loscha, Karin; Jaudzems, Kristaps; Ioannou, Charikleia; Su, Xun-Cheng; Dixon, Nicholas
Citation:

Citation: Loscha, Karin; Jaudzems, Kristaps; Ioannou, Charikleia; Su, Xun-Cheng; Hill, Flynn; Otting, Gottfried; Dixon, Nicholas; Liepinsh, Edvards. "A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader"  Nucleic Acids Res. 37, 2395-2404 (2009).
PubMed: 19255093

Assembly members:

Assembly members:
DnaI N-domain, polymer, 106 residues, 12543.353 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Bacillus subtilis   Taxonomy ID: 1423   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Bacillus subtilis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pKL1272

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DnaI N-domain: MEPIGRSLQGVTGRPDFQKR LEQMKEKVMKDQDVQAFLKE NEEVIDQKMIEKSLNKLYEY IEQSKNCSYCSEDENCNNLL EGYHPKLVVNGRSIDIEYYE CPVKRK

Data sets:
Data typeCount
15N chemical shifts114
1H chemical shifts771

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DnaI N-domain1
2ZINC ION2

Entities:

Entity 1, DnaI N-domain 106 residues - 12543.353 Da.

1   METGLUPROILEGLYARGSERLEUGLNGLY
2   VALTHRGLYARGPROASPPHEGLNLYSARG
3   LEUGLUGLNMETLYSGLULYSVALMETLYS
4   ASPGLNASPVALGLNALAPHELEULYSGLU
5   ASNGLUGLUVALILEASPGLNLYSMETILE
6   GLULYSSERLEUASNLYSLEUTYRGLUTYR
7   ILEGLUGLNSERLYSASNCYSSERTYRCYS
8   SERGLUASPGLUASNCYSASNASNLEULEU
9   GLUGLYTYRHISPROLYSLEUVALVALASN
10   GLYARGSERILEASPILEGLUTYRTYRGLU
11   CYSPROVALLYSARGLYS

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: entity_1, [U-95% 15N], 0.5 ± 0.05 mM; ZINC ION 0.5 ± 0.05 mM; D2O, [U-99% 2H], 10 ± 0.5 %; H2O 90 ± 0.5 %; sodium phosphate 10 ± 0.2 mM; sodium azide 0.1 ± 0.01 %; sodium chloride 100 ± 1 mM; DTT 1 ± 0.05 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 298.15 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Procheck, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho - data analysis

XEASY, Bartels et al. - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAI86406 BAM54146 BAM58975 GAK79927
EMBL CAA28633 CAA99605 CAB14858 CCU59399 CEI58128
GB AAA22405 AAC00359 ADV93692 AEP91897 AFI29422
REF NP_390776 WP_003229466 WP_014477627 WP_014480531 WP_014664931
SP P06567
AlphaFold P06567

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SPARKY: Backbone or all simulated peaks