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BMRB Entry 15444

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15444
MolProbity Validation Chart

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Title: solution structure of DNA binding domain of ngTRF1   PubMed: 18367475

Deposition date: 2007-08-27 Original release date: 2008-08-27

Authors: Lee, Weontae; Ko, Sunggeon

Citation: Ko, Sunggeon; Jun, Sung-Hoon; Bae, Hansol; Byun, Jung-Sue; Han, Woong; Park, Heeyoung; Yang, Seong Wook; Park, Sam-Yong; Jeon, Young Ho; Cheong, Chaejoon; Kim, Woo Taek; Lee, Weontae; Cho, Hyun-Soo. "Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins"  Nucleic Acids Res. 36, 2739-2755 (2008).

Assembly members:
NgTRF1, polymer, 121 residues, 13917.033 Da.

Natural source:   Common Name: Nicotiana tabacum   Taxonomy ID: 4097   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Nicotiana tabacum

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

Entity Sequences (FASTA):
NgTRF1: PVNQKSKRSELSQRRIRRPF SVAEVEALVEAVEHLGTGRW RDVKMRAFDNADHRTYVDLK DKWKTLVHTASIAPQQRRGE PVPQDLLDRVLAAHAYWSQQ QGKQHVEPLKILDAKAQKVG A

Data sets:
Data typeCount
13C chemical shifts423
15N chemical shifts114
1H chemical shifts550

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 121 residues - 13917.033 Da.

1   PROVALASNGLNLYSSERLYSARGSERGLU
2   LEUSERGLNARGARGILEARGARGPROPHE
3   SERVALALAGLUVALGLUALALEUVALGLU
4   ALAVALGLUHISLEUGLYTHRGLYARGTRP
5   ARGASPVALLYSMETARGALAPHEASPASN
6   ALAASPHISARGTHRTYRVALASPLEULYS
7   ASPLYSTRPLYSTHRLEUVALHISTHRALA
8   SERILEALAPROGLNGLNARGARGGLYGLU
9   PROVALPROGLNASPLEULEUASPARGVAL
10   LEUALAALAHISALATYRTRPSERGLNGLN
11   GLNGLYLYSGLNHISVALGLUPROLEULYS
12   ILELEUASPALALYSALAGLNLYSVALGLY
13   ALA

Samples:

sample_1: NgTRF1, [U-100% 15N], 1 mM; sodium phosphate 25 mM; NaCl 100 mM; H2O 90%; D2O 10%

sample_2: NgTRF1, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 25 mM; NaCl 100 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1

Software:

CYANA v2.2.5, P.GUNTERT ET AL. - refinement, structure solution

CYANA v2.4, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

CYANA v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CYANA v3.114, Goddard - peak picking

CYANA v3.1, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

CYANA v1.0, Cornilescu, Delaglio and Bax - data analysis

CYANA v2.6, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker DRX 600 MHz

Related Database Links:

PDB
GB AAN39330
REF XP_009615640 XP_009799099

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