BMRB Entry 18699

Name: DIMERIC PIL-E G-QUADRUPLEX DNA FROM NEISSERIA GONORRHOEAE, N STRUCTURES
Published: 2012-11-02

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PDB ID: 2lxv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18699
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: DIMERIC PIL-E G-QUADRUPLEX DNA FROM NEISSERIA GONORRHOEAE, N STRUCTURES PubMed: 23085077

Deposition date: 2012-08-31 Original release date: 2012-11-02

Authors: Kuryavyi, V.; Patel, D.

Citation: Kuryavyi, Vitaly; Cahoon, Laty; Seifert, H. Steven; Patel, Dinshaw. "RecA-binding pilE G4 sequence essential for pilin antigenic variation forms monomeric and 5' end-stacked dimeric parallel G-quadruplexes." Structure 20, 2090-2102 (2012).

Assembly members:
5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP, polymer, 16 residues, 5122.327 Da.

Natural source: Common Name: Neisseria Gonorrhoeae Taxonomy ID: 485 Superkingdom: Bacteria Kingdom: not available Genus/species: Neisseria Gonorrhoeae

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP: GGGTGGGTTGGGTGGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	134

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	di_PIL-E, chain 1	1
2	di_PIL-E, chain 2	1

Entities:

Entity 1, di_PIL-E, chain 1 16 residues - 5122.327 Da.

1

DG

DT

DG

DT

DG

2

DG

DT

DG

Samples:

sample_1: di_PIL-E0.3 – 3.5 mM; sodium chloride 100 mM; sodium phosphate 5 mM; D2O 10%; H2O 90%

sample_2: di_PIL-E0.3 – 3.5 mM; D2O, [U-100% 2H], 100%; sodium chloride 100 mM; sodium phosphate 5 mM

sample_conditions_1: ionic strength: 0.105 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-1H NOESY	sample_1	isotropic	sample_conditions_1
1H-15N JRHMQC	sample_1	isotropic	sample_conditions_1
1H-15N HMBC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
1H-31P COSY	sample_2	isotropic	sample_conditions_1

Software:

X-PLOR v3.851, BRUNGER, SCHWIETERS, KUSZEWSKI, TJ - refinement

NMR spectrometers:

Varian INOVA 600 MHz
Bruker Avance 800 MHz