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 25752

Title: Backbone assignments and ILV methyl assignments for EcoRV bound to 16-mer double stranded DNA (GCAAAGATATCTTTCG) with Lu3+   PubMed: 27786446

Authors: Sinha, Kaustubh; Sangani, Sahil; Rule, Gordon; Jen-Jacobson, Linda

Citation: Sinha, Kaustubh; Sangani, Sahil; Kehr, Andrew; Rule, Gordon; Jen-Jacobson, Linda. "Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.'"  Biochemistry 55, 6115-6132 (2016).

Assembly members:
EcoRV, polymer, 244 residues, 28650 Da.
5'-GCAAAGATATCTTTCG-3', polymer, 16 residues, 9760 Da.
LUTETIUM (III) ION, non-polymer, 174.967 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

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

Entity Sequences (FASTA):
EcoRV: SLRSDLINALYDENQKYDVC GIISAEGKIYPLGSDTKVLS TIFELFSRPIINKIAEKHGY IVEEPKQQNHYPDFTLYKPS EPNKKIAIDIKTTYTNKENE KIKFTLGGYTSFIRNNTKNI VYPFDQYIAHWIIGYVYTRV ATRKSSLKTYNINELNEIPK PYKGVKVFLQDKWVIAGDLA GSGNTTNIGSIHAHYKDFVE GKGIFDSEDEFLDYWRNYER TSQLRNDKYNNISEYRNWIY RGRK
5'-GCAAAGATATCTTTCG-3': GCAAAGATATCTTTCG

Data sets:
Data typeCount
13C chemical shifts371
15N chemical shifts117
1H chemical shifts291

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RV dimer, 11
2RV dimer, 21
3AAA DNA fragment, 12
4AAA DNA fragment, 22
5Lutetium ion, 13
6Lutetium ion, 23
7Lutetium ion, 33

Entities:

Entity 1, RV dimer, 1 244 residues - 28650 Da.

1   SERLEUARGSERASPLEUILEASNALALEU
2   TYRASPGLUASNGLNLYSTYRASPVALCYS
3   GLYILEILESERALAGLUGLYLYSILETYR
4   PROLEUGLYSERASPTHRLYSVALLEUSER
5   THRILEPHEGLULEUPHESERARGPROILE
6   ILEASNLYSILEALAGLULYSHISGLYTYR
7   ILEVALGLUGLUPROLYSGLNGLNASNHIS
8   TYRPROASPPHETHRLEUTYRLYSPROSER
9   GLUPROASNLYSLYSILEALAILEASPILE
10   LYSTHRTHRTYRTHRASNLYSGLUASNGLU
11   LYSILELYSPHETHRLEUGLYGLYTYRTHR
12   SERPHEILEARGASNASNTHRLYSASNILE
13   VALTYRPROPHEASPGLNTYRILEALAHIS
14   TRPILEILEGLYTYRVALTYRTHRARGVAL
15   ALATHRARGLYSSERSERLEULYSTHRTYR
16   ASNILEASNGLULEUASNGLUILEPROLYS
17   PROTYRLYSGLYVALLYSVALPHELEUGLN
18   ASPLYSTRPVALILEALAGLYASPLEUALA
19   GLYSERGLYASNTHRTHRASNILEGLYSER
20   ILEHISALAHISTYRLYSASPPHEVALGLU
21   GLYLYSGLYILEPHEASPSERGLUASPGLU
22   PHELEUASPTYRTRPARGASNTYRGLUARG
23   THRSERGLNLEUARGASNASPLYSTYRASN
24   ASNILESERGLUTYRARGASNTRPILETYR
25   ARGGLYARGLYS

Entity 2, AAA DNA fragment, 1 16 residues - 9760 Da.

1   DGDCDADADADGDADTDADT
2   DCDTDTDTDCDG

Entity 3, Lutetium ion, 1 - Lu - 174.967 Da.

1   LU

Samples:

sample_1: EcoRV, [U-99% 13C; U-99% 15N; U-99% 2H], 1 mM; 5'-GCAAAGATATCTTTCG-3', n/a, 0.5 mM; entity_LU, n/a, 2.2 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: EcoRV, [ILV-13CH3 ; U-99% 15N; U-99% 2H], 0.5 mM; 5'-GCAAAGATATCTTTCG-3', n/a, 0.5 mM; entity_LU, n/a, 2.2 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: EcoRV, [ILV-13CH3 ; U-99% 15N; U-99% 2H], 0.5 mM; 5'-GCAAAGATATCTTTCG-3', n/a, 0.5 mM; entity_LU, n/a, 2.2 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCBsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
4D ILV methyl NOEsample_2isotropicsample_conditions_1
ILV-HMCMCGsample_3isotropicsample_conditions_1
ILV-HMCM[CG]CBsample_3isotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

TOPSPIN, Bruker Biospin - collection

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

Monte v2.03, Rule - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 700 MHz

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