BMRB Entry 19986

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19986
MolProbity Validation Chart

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Title:
NMR structure of Xenopus RecQ4 zinc knuckle
Deposition date:
2014-05-23
Original release date:
2015-08-03
Authors:
Zucchelli, Chiara; Marino, Francesca; Mojumdar, Aditya; Onesti, Silvia; Musco, Giovanna
Citation:

Citation: Marino, Francesca; Mojumdar, Aditya; Zucchelli, Chiara; Musco, Giovanna; Buratti, Emanuele; Vindigni, Alessandro; Onesti, Silvia. "A novel RNA/DNA binding motif in the N-terminal domain of RecQ4"  Nucleic Acids Res. ., .-..

Assembly members:

Assembly members:
RecQ4_zinc_knuckle, polymer, 25 residues, 2613.915 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: African clawed frog   Taxonomy ID: 8355   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Xenopus laevis

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RecQ4_zinc_knuckle: NRSGDTCFRCGGMGHWASQC PGSVP

Data sets:
Data typeCount
13C chemical shifts43
15N chemical shifts21
1H chemical shifts140

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1RecQ4_zinc_knuckle1
2ZINC ION2

Entities:

Entity 1, RecQ4_zinc_knuckle 25 residues - 2613.915 Da.

1   ASNARGSERGLYASPTHRCYSPHEARGCYS
2   GLYGLYMETGLYHISTRPALASERGLNCYS
3   PROGLYSERVALPRO

Entity 2, ZINC ION - 65.409 Da.

1   ZN

Samples:

sample_1: RecQ4 zinc knuckle 1.1 mM; ZnCl2 1.25 mM; D2O, [U-100% 2H], 10%; sodium phosphate pH 6.3 20 mM; potassium chloride 150 mM; DTT 4 mM; DSS 0.3 mM; H2O 90%

sample_conditions_1: ionic strength: 170 mM; pH: 6.3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
1D 1Hsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

TOPSPIN v2.0, Bruker Biospin - collection

CcpNMR v2.5.1, CCPN - chemical shift assignment, peak picking

ARIA v2.3.1, Linge, O'Donoghue and Nilges - refinement, structure solution

TALOS, Cornilescu, Delaglio and Bax - dihedral angle calculations

ProcheckNMR, Laskowski and MacArthur - geometry optimization, refinement

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAE48358
GB AAI61707 AAY89585
REF NP_001089101 NP_001089182

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