BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 11038

Title: The DNA binding domain of RTBP1   PubMed: 19152316

Deposition date: 2008-03-22 Original release date: 2009-04-29

Authors: Lee, Weontae; Ko, Sunggeon

Citation: Ko, Sunggeon; Yu, Eun Young; Shin, Joon; Yoo, Hyun Hee; Tanaka, Toshiyuki; Kim, Woo Taek; Cho, Hyun-Soo; Lee, Weontae; Chung, In Kwon. "Solution structure of the DNA binding domain of rice telomere binding protein RTBP1"  Biochemistry 48, 827-838 (2009).

Assembly members:
The DNA binding domain of RTBP1, polymer, 122 residues, 13862.927 Da.

Natural source:   Common Name: Oryza sativa   Taxonomy ID: 4530   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Oryza sativa

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PGEX 4T-1

Entity Sequences (FASTA):
The DNA binding domain of RTBP1: GSPFADPNSLALANVPLSRS KRPDFGQRRIRRPFTVAEVE LLVEAVEHLGTGRWRDVKFR AFENVHHRTYVDLKDKWKTL VHTASIAPQQRRGAPVPQEL LDRVLAAQAYWSVDSSGRIV TL

Data sets:
Data typeCount
13C chemical shifts409
15N chemical shifts113
1H chemical shifts678

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1The DNA binding domain of RTBP11

Entities:

Entity 1, The DNA binding domain of RTBP1 122 residues - 13862.927 Da.

First G and S and "VDSSGRIVTL" in C-terminal were from cloining artifacts.

1   GLYSERPROPHEALAASPPROASNSERLEU
2   ALALEUALAASNVALPROLEUSERARGSER
3   LYSARGPROASPPHEGLYGLNARGARGILE
4   ARGARGPROPHETHRVALALAGLUVALGLU
5   LEULEUVALGLUALAVALGLUHISLEUGLY
6   THRGLYARGTRPARGASPVALLYSPHEARG
7   ALAPHEGLUASNVALHISHISARGTHRTYR
8   VALASPLEULYSASPLYSTRPLYSTHRLEU
9   VALHISTHRALASERILEALAPROGLNGLN
10   ARGARGGLYALAPROVALPROGLNGLULEU
11   LEUASPARGVALLEUALAALAGLNALATYR
12   TRPSERVALASPSERSERGLYARGILEVAL
13   THRLEU

Samples:

sample_1: The DNA binding domai of RTBP1, [U-99% 15N], 1 mM; Potassium phosphate 50 mM; NaCl 100 mM; NaN3 1 mM; H2O 90%; D2O 10%

sample_2: The DNA binding domai of RTBP1, [U-100% 13C], 1 mM; Potassium phosphate 50 mM; NaCl 100 mM; NaN3 1 mM; D2O 100%

sample_3: The DNA binding domai of RTBP1, [U-99% 13C; U-99% 15N], 1 mM; Potassium phosphate 50 mM; NaCl 100 mM; NaN3 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; pressure: 1 Pa; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1

Software:

CYANA v2.2.5, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

CYANA, Bruker Biospin - processing

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

CYANA, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

CYANA, Goddard - chemical shift assignment, peak picking

CYANA, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker DRX 900 MHz

Related Database Links:

PDB
GB AAF97508 EAY88030 EAZ25089
SP Q9LL45
AlphaFold Q9LL45

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