BMRB Entry 17689

Name: Novel dimeric structure of phage phi29-encoded protein p56: Insights into Uracil-DNA glycosylase inhibition
Published: 2012-02-22

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PDB ID: 2le2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17689
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

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:

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).
PubMed: 21890898

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pT7-3-p56-phi29

Entity Sequences (FASTA):

Entity Sequences (FASTA):
p56: MVQNDFVDSYDVTMLLQDDD GKQYYEYHKGLSLSDFEVLY GNTADEIIKLRLDKVL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	58
1H chemical shifts	391

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	p56 chain A	1
2	p56 chain B	1

Entities:

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

1

MET

VAL

GLN

ASN

ASP

PHE

VAL

ASP

SER

TYR

2

ASP

VAL

THR

MET

LEU

GLN

ASP

3

GLY

LYS

GLN

TYR

GLU

TYR

HIS

LYS

GLY

4

LEU

SER

LEU

SER

ASP

PHE

GLU

VAL

LEU

TYR

5

GLY

ASN

THR

ALA

ASP

GLU

ILE

LYS

LEU

6

ARG

LEU

ASP

LYS

VAL

LEU

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_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

PDB	2LE2 3ZOQ
EMBL	CAA24477
GB	ACE96021
REF	YP_002004527