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 15083

Title: NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element   PubMed: 17481658

Authors: Doucleff, M.; Pelton, J.; Lee, P.; Wemmer, D.

Citation: Doucleff, M.; Pelton, J.; Lee, P.; Nixon, B.; Wemmer, D.. "Structural basis of DNA recognition by the alternative sigma-factor, sigma54"  J. Mol. Biol. 369, 1070-1078 (2007).

Assembly members:
NIRB_SIGMA-54_BINDING_SITE_NON-TEMPLATE_STRAND, polymer, 14 residues, 4364.794 Da.
NIRB_SIGMA-54_BINDING_SITE_TEMPLATE_STRAND, polymer, 14 residues, 4514.872 Da.
RNA_POLYMERASE_SIGMA_FACTOR_RPON, polymer, 63 residues, 7490.880 Da.

Natural source:   Common Name: Aquifex aeolicus   Taxonomy ID: 63363   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Aquifex aeolicus

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
NIRB_SIGMA-54_BINDING_SITE_NON-TEMPLATE_STRAND: TTTTGGCACGTTTC
NIRB_SIGMA-54_BINDING_SITE_TEMPLATE_STRAND: GAAACGTGCCAAAA
RNA_POLYMERASE_SIGMA_FACTOR_RPON: HMLTQGELMKLIKEIVENED KRKPYSDQEIANILKEKGFK VARRTVAKYREMLGIPSSRE RRI

Data sets:
Data typeCount
13C chemical shifts208
15N chemical shifts61
1H chemical shifts663

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1-24 ELEMENT NON-TEMPLATE STRAND1
2-24 ELEMENT TEMPLATE STRAND2
3C-TERMINAL RPON DOMAIN3

Entities:

Entity 1, -24 ELEMENT NON-TEMPLATE STRAND 14 residues - 4364.794 Da.

1   DTDTDTDTDGDGDCDADCDG
2   DTDTDTDC

Entity 2, -24 ELEMENT TEMPLATE STRAND 14 residues - 4514.872 Da.

1   DGDADADADCDGDTDGDCDC
2   DADADADA

Entity 3, C-TERMINAL RPON DOMAIN 63 residues - 7490.880 Da.

1   HISMETLEUTHRGLNGLYGLULEUMETLYS
2   LEUILELYSGLUILEVALGLUASNGLUASP
3   LYSARGLYSPROTYRSERASPGLNGLUILE
4   ALAASNILELEULYSGLULYSGLYPHELYS
5   VALALAARGARGTHRVALALALYSTYRARG
6   GLUMETLEUGLYILEPROSERSERARGGLU
7   ARGARGILE

Samples:

sample_1: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND 1 ± 0.2 mM; NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND 1 ± 0.2 mM; RNA POLYMERASE SIGMA FACTOR RPON, [U-100% 13C; U-100% 15N], 1 ± 0.2 mM; HEPES, [U-99% 2H], 10 ± 0.1 mM; EDTA 1 ± 0.1 mM; NaCl 250 ± 0.1 mM

sample_2: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND 1 ± .2 mM; NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND 1 ± .2 mM; RNA POLYMERASE SIGMA FACTOR RPON, [U-100% 13C; U-100% 15N], 1 ± .2 mM; HEPES 10 ± .1 mM; EDTA 1 ± .1 mM; NaCl 250 ± .2 mM

sample_3: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND 1 ± .2 mM; NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND 1 ± .2 mM; RNA POLYMERASE SIGMA FACTOR RPON 1 ± .2 mM; HEPES 10 ± .1 mM; EDTA 1 ± .1 mM; NaCl 250 ± .1 mM

sample_conditions_1: ionic strength: 250 mM; pH: 6.9; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 250 mM; pH: 6.9; pressure: 1 atm; temperature: 318 K

Experiments:

NameSampleSample stateSample conditions
3D_C13-seperated[F1], C12-filtered[F2] NOESYsample_1isotropicsample_conditions_2
3D_C13-seperated_NOESYsample_2isotropicsample_conditions_1
3D_15N-seperated_NOESYsample_3isotropicsample_conditions_1
2D_C12-filtered[F1,F2] NOESYsample_1isotropicsample_conditions_2
2D_C12-filtered[F1] NOESYsample_1isotropicsample_conditions_2
3D HNCAsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_2
3D HNHAsample_3isotropicsample_conditions_1

Software:

CNS, Bruker Biospin - collection

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

CNS v5.0.4, Johnson, One Moon Scientific - data analysis

CNS v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v2.14, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker DMX 800 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
GB AAC06814
REF NP_213418 WP_010880356