BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17689

Title: Novel dimeric structure of phage phi29-encoded protein p56: Insights into Uracil-DNA glycosylase inhibition   PubMed: 21890898

Deposition date: 2011-06-06 Original release date: 2012-02-22

Authors: Asensio, Juan Luis; Perez-Lago, Laura; M. Lazaro, Jose; Gonzalez, Carlos; Serrano-Heras, Gemma; Salas, Margarita

Citation: Asensio, Juan Luis; Perez-Lago, Laura; Lazaro, Jose; Gonzalez, Carlos; Serrano-Heras, Gemma; Salas, Margarita. "Novel dimeric structure of phage 29-encoded protein p56: insights into uracil-DNA glycosylase inhibition."  Nucleic Acids Res. 39, 9779-9788 (2011).

Assembly members:
p56, polymer, 56 residues, 6571.369 Da.

Natural source:   Common Name: Bacteriophage phi-29   Taxonomy ID: 10756   Superkingdom: Viruses   Kingdom: not available   Genus/species: Bacteriophage phi29

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

Entity Sequences (FASTA):
p56: MVQNDFVDSYDVTMLLQDDD GKQYYEYHKGLSLSDFEVLY GNTADEIIKLRLDKVL

Data sets:
Data typeCount
15N chemical shifts58
1H chemical shifts391

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1p56 chain A1
2p56 chain B1

Entities:

Entity 1, p56 chain A 56 residues - 6571.369 Da.

1   METVALGLNASNASPPHEVALASPSERTYR
2   ASPVALTHRMETLEULEUGLNASPASPASP
3   GLYLYSGLNTYRTYRGLUTYRHISLYSGLY
4   LEUSERLEUSERASPPHEGLUVALLEUTYR
5   GLYASNTHRALAASPGLUILEILELYSLEU
6   ARGLEUASPLYSVALLEU

Samples:

sample_1: p56 0.5 mM; sodium chloride 100 mM; potassium phosphate 10 mM; H2O 90%; D2O 90%

sample_2: p56, [U-98% 13C; U-98% 15N], 0.5 mM; sodium chloride 100 mM; potassium phosphate 10 mM; H2O 90%; D2O 90%

sample_3: p56 0.5 mM; sodium chloride 100 mM; potassium phosphate 10 mM; H2O 90%; D2O 90%

sample_conditions_1: ionic strength: 0.13 M; pH: 5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1

Software:

XEASY, Bartels et al. - data analysis

DYANA, Guntert, Braun and Wuthrich - structure solution

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

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker DMX 600 MHz

Related Database Links:

PDB
EMBL CAA24477
GB ACE96021
REF YP_002004527

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts