BMRB Entry 34291

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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/BMR34291
MolProbity Validation Chart

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Title:
NMR structure of the DNA-bound helix bundle domain from the functional pRN1 primase
Deposition date:
2018-06-21
Original release date:
2018-12-19
Authors:
Boudet, J.; Lipps, G.; Allain, F.
Citation:

Citation: Boudet, J.; Devillier, J.; Wiegand, T.; Salmon, L.; Meier, B.; Lipps, G.; Allain, F.. "A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template"  Cell 176, 154-166 (2019).
PubMed: 30595448

Assembly members:

Assembly members:
entity_1, polymer, 9 residues, 2706.785 Da.
entity_2, polymer, 115 residues, 13528.738 Da.

Natural source:

Natural source:   Common Name: Sulfolobus islandicus   Taxonomy ID: 43080   Superkingdom: Archaea   Kingdom: not available   Genus/species: Sulfolobus islandicus

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CTGTGCTCA
entity_2: TVVEFEELRKELVKRDSGKP VEKIKEEICTKSPPKLIKEI ICENKTYADVNIDRSRGDWH VILYLMKHGVTDPDKILELL PRDSKAKENEKWNTQKYFVI TLSKAWSVVKKYLEA

Data sets:
Data typeCount
13C chemical shifts303
15N chemical shifts104
1H chemical shifts779

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 9 residues - 2706.785 Da.

1   DCDTDGDTDGDCDTDCDA

Entity 2, entity_2 115 residues - 13528.738 Da.

1   THRVALVALGLUPHEGLUGLULEUARGLYS
2   GLULEUVALLYSARGASPSERGLYLYSPRO
3   VALGLULYSILELYSGLUGLUILECYSTHR
4   LYSSERPROPROLYSLEUILELYSGLUILE
5   ILECYSGLUASNLYSTHRTYRALAASPVAL
6   ASNILEASPARGSERARGGLYASPTRPHIS
7   VALILELEUTYRLEUMETLYSHISGLYVAL
8   THRASPPROASPLYSILELEUGLULEULEU
9   PROARGASPSERLYSALALYSGLUASNGLU
10   LYSTRPASNTHRGLNLYSTYRPHEVALILE
11   THRLEUSERLYSALATRPSERVALVALLYS
12   LYSTYRLEUGLUALA

Samples:

sample_1: DNA-bound helix bundle domain, [U-99% 13C; U-99% 15N], 1.0 ± 0.1 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 ± 0.1 mM; NaCl 100 mM

sample_2: DNA-bound helix bundle domain, [U-100% 13C], 0.7 ± 0.1 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 0.7 ± 0.1 mM; NaCl 100 mM

sample_3: DNA-bound helix bundle domain, [U-99% 15N], 1.1 ± 0.1 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.1 ± 0.1 mM; NaCl 50 mM

sample_4: DNA-bound helix bundle domain 1.0 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 mM; NaCl 50 mM

sample_conditions_1: ionic strength: 100 mM; pH: 5.5; pressure: 1 atm; temperature: 323 K

sample_conditions_2: ionic strength: 100 mM; pH: 5.5; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_2
2D 1H-15N HSQCsample_3isotropicsample_conditions_3
3D 1H-15N NOESYsample_3isotropicsample_conditions_2
3D 1H-15N NOESYsample_3isotropicsample_conditions_3
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_2
2D 1H-1H TOCSYsample_4isotropicsample_conditions_1
2D 1H-1H TOCSYsample_4isotropicsample_conditions_2
2D-F1fF2f-NOESYsample_2isotropicsample_conditions_1
2D-F2f-NOESYsample_2isotropicsample_conditions_1
3D 13C-aliphatic Hfiltered-Hedited NOESYsample_2isotropicsample_conditions_1
3D 13C-aromatic Hfiltered-Hedited NOESYsample_2isotropicsample_conditions_1
3D 13C-aliphatic Hfiltered-Hedited NOESYsample_2isotropicsample_conditions_2
3D 13C-aromatic Hfiltered-Hedited NOESYsample_2isotropicsample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment, data analysis

CANDID, Herrmann, Guntert and Wuthrich - peak picking

TOPSPIN, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker AVANCE III HD 900 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE III 600 MHz

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