BMRB Entry 30567

Name: NMR Structure of the DNA binding domain of EhMybS3
Published: 2020-02-07

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PDB ID: 6nvz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30567
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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:

NMR Structure of the DNA binding domain of EhMybS3

Deposition date:

2019-02-05

Original release date:

2020-02-07

Authors:

Titaux-Delgado, G.; del Rio-Portilla, F.

Citation:

Citation: Cardenas-Hernandez, H.; Titaux-Delgado, G.; Castaneda-Ortiz, E.; Torres-Larios, A.; Brieba, L.; de Rio-portilla, F.; Azuara-Liceaga, E.. "Genome-wide and structural analysis of the Myb-SHAQKYF family in Entamoeba histolytica" Biochim. Biophys. Acta Proteins Proteom. 1869, 140601-140601 (2021).
PubMed: 33422669

Assembly members:

Assembly members:
entity_1, polymer, 60 residues, 6986.167 Da.

Natural source:

Natural source: Common Name: Entamoeba histolytica Taxonomy ID: 5759 Superkingdom: Eukaryota Kingdom: not available Genus/species: Entamoeba histolytica

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPLGSKKREVWTDAEHAKFV EGLALFHKDWKKIKEYIGTK TVVQIRSHAQKYFLKLNKTA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
1H chemical shifts	355

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 60 residues - 6986.167 Da.

1	GLY	PRO	LEU	GLY	SER	LYS	LYS	ARG	GLU	VAL
2	TRP	THR	ASP	ALA	GLU	HIS	ALA	LYS	PHE	VAL
3	GLU	GLY	LEU	ALA	LEU	PHE	HIS	LYS	ASP	TRP
4	LYS	LYS	ILE	LYS	GLU	TYR	ILE	GLY	THR	LYS
5	THR	VAL	VAL	GLN	ILE	ARG	SER	HIS	ALA	GLN
6	LYS	TYR	PHE	LEU	LYS	LEU	ASN	LYS	THR	ALA

Samples:

sample_1: EhMybS3 1.5 mM

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 298 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

Software:

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CARA v1.8, Keller and Wuthrich - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

NMR spectrometers:

Bruker AMX 700 MHz

1	GLY	PRO	LEU	GLY	SER	LYS	LYS	ARG	GLU	VAL
2	TRP	THR	ASP	ALA	GLU	HIS	ALA	LYS	PHE	VAL
3	GLU	GLY	LEU	ALA	LEU	PHE	HIS	LYS	ASP	TRP
4	LYS	LYS	ILE	LYS	GLU	TYR	ILE	GLY	THR	LYS
5	THR	VAL	VAL	GLN	ILE	ARG	SER	HIS	ALA	GLN
6	LYS	TYR	PHE	LEU	LYS	LEU	ASN	LYS	THR	ALA

1	GLY	PRO	LEU	GLY	SER	LYS	LYS	ARG	GLU	VAL
2	TRP	THR	ASP	ALA	GLU	HIS	ALA	LYS	PHE	VAL
3	GLU	GLY	LEU	ALA	LEU	PHE	HIS	LYS	ASP	TRP
4	LYS	LYS	ILE	LYS	GLU	TYR	ILE	GLY	THR	LYS
5	THR	VAL	VAL	GLN	ILE	ARG	SER	HIS	ALA	GLN
6	LYS	TYR	PHE	LEU	LYS	LEU	ASN	LYS	THR	ALA

1	GLY	PRO	LEU	GLY	SER	LYS	LYS	ARG	GLU	VAL
2	TRP	THR	ASP	ALA	GLU	HIS	ALA	LYS	PHE	VAL
3	GLU	GLY	LEU	ALA	LEU	PHE	HIS	LYS	ASP	TRP
4	LYS	LYS	ILE	LYS	GLU	TYR	ILE	GLY	THR	LYS
5	THR	VAL	VAL	GLN	ILE	ARG	SER	HIS	ALA	GLN
6	LYS	TYR	PHE	LEU	LYS	LEU	ASN	LYS	THR	ALA