BMRB Entry 25092

Title:
truncated EcMazE-DNA complex
Deposition date:
2014-07-15
Original release date:
2015-02-02
Authors:
Zorzini, Valentina; Buts, Lieven; Loris, Remy; van Nuland, Nico
Citation:

Citation: Zorzini, Valentina; Buts, Lieven; Schrank, Evelyne; Sterckx, Yann; Respondek, Michal; Engelberg-Kulka, Hanna; Loris, Remy; Zangger, Klaus; van Nuland, Nico. "Escherichia coli antitoxin MazE as transcription factor: insights into MazE-DNA binding"  Nucleic Acids Res. 43, 1241-1256 (2015).
PubMed: 25564525

Assembly members:

Assembly members:
entity_1, polymer, 67 residues, 5558.510 Da.
DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3'), polymer, 15 residues, 4624.059 Da.
DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3'), polymer, 15 residues, 4553.023 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pQE30-mazE

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: NHKVHHHHHHMSDDDDKGIH SSVKRWGNSPAVRIPATLMQ ALNLNIDDEVKIDLVDGKLI IEPVRKE
DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3'): CGTGATATATAGTGC
DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3'): GCACTATATATCACG

Data sets:
Data typeCount
1H chemical shifts65
15N chemical shifts61

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1_11
2entity_1_21
3DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')2
4DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')3

Entities:

Entity 1, entity_1_1 67 residues - 5558.510 Da.

1   ASNHISLYSVALHISHISHISHISHISHIS
2   METSERASPASPASPASPLYSGLYILEHIS
3   SERSERVALLYSARGTRPGLYASNSERPRO
4   ALAVALARGILEPROALATHRLEUMETGLN
5   ALALEUASNLEUASNILEASPASPGLUVAL
6   LYSILEASPLEUVALASPGLYLYSLEUILE
7   ILEGLUPROVALARGLYSGLU

Entity 2, DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3') 15 residues - 4624.059 Da.

1   DCDGDTDGDADTDADTDADT
2   DADGDTDGDC

Entity 3, DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3') 15 residues - 4553.023 Da.

1   DGDCDADCDTDADTDADTDA
2   DTDCDADCDG

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.33 – 0.4 mM; DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')0 – 0.4 mM; DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')0 – 0.4 mM; potassium phosphate 50 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_conditions_1: temperature: 298 K; pH: 6.5; pressure: 1 atm; ionic strength: 50 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

CcpNMR, CCPN - data analysis

Haddock, Alexandre Bonvin - structure solution, refinement

NMR spectrometers:

  • Varian VNMRS 600 MHz

Related Database Links:

BMRB 25086 25093 25094
PDB
DBJ BAA41177 BAB37066 BAE76857 BAG78565 BAI27044
EMBL CAP77216 CAQ33107 CAQ87849 CAQ99711 CAR04293
GB AAA03238 AAA69293 AAC75825 AAG57896 AAZ89539
REF NP_311670 NP_417263 WP_000581935 WP_000581936 WP_000581937
SP P0AE72 P0AE73
AlphaFold P0AE73 P0AE72

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