BMRB Entry 15083

Name: NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element
Published: 2007-10-17

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PDB ID: 2o8k
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR15083
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element

Deposition date:

2006-12-19

Original release date:

2007-10-17

Authors:

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

Citation:

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).
PubMed: 17481658

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	208
15N chemical shifts	61
1H chemical shifts	663

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	-24 ELEMENT NON-TEMPLATE STRAND	1
2	-24 ELEMENT TEMPLATE STRAND	2
3	C-TERMINAL RPON DOMAIN	3

Entities:

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

1

DT

DG

DC

DA

DC

DG

2

DT

DC

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

1

DG

DA

DC

DG

DT

DG

DC

2

DA

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

1

HIS

MET

LEU

THR

GLN

GLY

GLU

LEU

MET

LYS

2

LEU

ILE

LYS

GLU

ILE

VAL

GLU

ASN

GLU

ASP

3

LYS

ARG

LYS

PRO

TYR

SER

ASP

GLN

GLU

ILE

4

ALA

ASN

ILE

LEU

LYS

GLU

LYS

GLY

PHE

LYS

5

VAL

ALA

ARG

THR

VAL

ALA

LYS

TYR

ARG

6

GLU

MET

LEU

GLY

ILE

PRO

SER

ARG

GLU

7

ARG

ILE

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:

Name	Sample	Sample state	Sample conditions
3D_C13-seperated[F1], C12-filtered[F2] NOESY	sample_1	isotropic	sample_conditions_2
3D_C13-seperated_NOESY	sample_2	isotropic	sample_conditions_1
3D_15N-seperated_NOESY	sample_3	isotropic	sample_conditions_1
2D_C12-filtered[F1,F2] NOESY	sample_1	isotropic	sample_conditions_2
2D_C12-filtered[F1] NOESY	sample_1	isotropic	sample_conditions_2
3D HNCA	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D HNHA	sample_3	isotropic	sample_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

PDB	2AHQ 2O8K 2O9L
GB	AAC06814
REF	NP_213418 WP_010880356