BMRB Entry 15989

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15989
MolProbity Validation Chart

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Title:
Solution NMR structure of the R2R3 DNA binding domain of Myb1 protein from protozoan parasite Trichomonas vaginalis
Deposition date:
2008-10-16
Original release date:
2009-04-04
Authors:
Lou, Yuan-Chao; Wei, Shu-Yi; Rajasekaran, M.; Chou, Chun-Chi; Hsu, Hong-Ming; Tai, Jung-Hsiang; Chen, Chinpan
Citation:

Citation: Lou, Yuan-Chao; Wei, Shu-Yi; Rajasekaran, M.; Chou, Chun-Chi; Hsu, Hong-Ming; Tai, Jung-Hsiang; Chen, Chinpan. "NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis"  Nucleic Acids Res. 37, 2381-2394 (2009).
PubMed: 19246540

Assembly members:

Assembly members:
R2R3 DNA binding domain, polymer, 107 residues, 13218.344 Da.

Natural source:

Natural source:   Common Name: Trichomonas vaginalis   Taxonomy ID: 5722   Superkingdom: Eukaryota   Kingdom: not available   Genus/species: Trichomonas vaginalis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET29b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
R2R3 DNA binding domain: KVKFTEEEDLKLQQLVMRYG AKDWIRISQLMITRNPRQCR ERWNNYINPALRTDPWSPEE DMLLDQKYAEYGPKWNKISK FLKNRSDNNIRNRWMMIARH RAKHQKS

Data sets:
Data typeCount
13C chemical shifts493
15N chemical shifts121
1H chemical shifts789
heteronuclear NOE values92

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1R2R3 DNA binding domain1

Entities:

Entity 1, R2R3 DNA binding domain 107 residues - 13218.344 Da.

1   LYSVALLYSPHETHRGLUGLUGLUASPLEU
2   LYSLEUGLNGLNLEUVALMETARGTYRGLY
3   ALALYSASPTRPILEARGILESERGLNLEU
4   METILETHRARGASNPROARGGLNCYSARG
5   GLUARGTRPASNASNTYRILEASNPROALA
6   LEUARGTHRASPPROTRPSERPROGLUGLU
7   ASPMETLEULEUASPGLNLYSTYRALAGLU
8   TYRGLYPROLYSTRPASNLYSILESERLYS
9   PHELEULYSASNARGSERASPASNASNILE
10   ARGASNARGTRPMETMETILEALAARGHIS
11   ARGALALYSHISGLNLYSSER

Samples:

sample_1: entity, [U-13C; U-15N], 1 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 mM; beta-mercaptoethanol 20 mM

sample_2: entity, [U-13C; U-15N], 1 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 mM; beta-mercaptoethanol 20 mM

sample_conditions_1: ionic strength: 0.17 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
2D 1H-15N HxNOEsample_1isotropicsample_conditions_1

Software:

NMRViewJ v8.0, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
GB AAX51243 EAY03723
REF XP_001315946

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