BMRB Entry 19380

Name: NMR structure of the RNA polymerase alpha subunit C-terminal domain from Helicobacter pylori
Published: 2014-02-13

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PDB ID: 2max
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19380
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of the RNA polymerase alpha subunit C-terminal domain from Helicobacter pylori PubMed: 24442709

Deposition date: 2013-07-21 Original release date: 2014-02-13

Authors: Borin, Brendan; Krezel, Andrzej

Citation: Borin, Brendan; Tang, Wei; Krezel, Andrzej. "Helicobacter pylori RNA polymerase -subunit C-terminal domain shows features unique to -proteobacteria and binds NikR/DNA complexes." Protein Sci. 23, 454-463 (2014).

Assembly members:
RNAP_alpha_subunit_CTD, polymer, 126 residues, 12754.470 Da.

Natural source: Common Name: e-proteobacteria Taxonomy ID: 210 Superkingdom: Bacteria Kingdom: not available Genus/species: Helicobacter pylori

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

Entity Sequences (FASTA):
RNAP_alpha_subunit_CTD: MRGSHHHHHHGSLGVFGERP IANTEYSGDYAQRDDAKDLS AKIESMNLSARCFNCLDKIG IKYVGELVLMSEEELKGVKN MGKKSYDEIAEKLNDLGYPV GTELSPEQRESLKKRLEKLE DKGGND

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	340
15N chemical shifts	112
1H chemical shifts	736

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA polymerase alpha subunit C-terminal domain	1

Entities:

Entity 1, RNA polymerase alpha subunit C-terminal domain 126 residues - 12754.470 Da.

residues 1-12 represent a non-native His6 Ni-affinity tag. Contains native residues 231-344.

1

MET

ARG

GLY

SER

HIS

2

GLY

SER

LEU

GLY

VAL

PHE

GLY

GLU

ARG

PRO

3

ILE

ALA

ASN

THR

GLU

TYR

SER

GLY

ASP

TYR

4

ALA

GLN

ARG

ASP

ALA

LYS

ASP

LEU

SER

5

ALA

LYS

ILE

GLU

SER

MET

ASN

LEU

SER

ALA

6

ARG

CYS

PHE

ASN

CYS

LEU

ASP

LYS

ILE

GLY

7

ILE

LYS

TYR

VAL

GLY

GLU

LEU

VAL

LEU

MET

8

SER

GLU

LEU

LYS

GLY

VAL

LYS

ASN

9

MET

GLY

LYS

SER

TYR

ASP

GLU

ILE

ALA

10

GLU

LYS

LEU

ASN

ASP

LEU

GLY

TYR

PRO

VAL

11

GLY

THR

GLU

LEU

SER

PRO

GLU

GLN

ARG

GLU

12

SER

LEU

LYS

ARG

LEU

GLU

LYS

LEU

GLU

13

ASP

LYS

GLY

ASN

ASP

Samples:

sample_1: RNAP alpha subunit CTD, [U-15N], 1 mM; potassium phosphate 25 mM; potassium chloride 225 mM; TCEP 1 mM; H2O 90%; D2O 10%

sample_2: RNAP alpha subunit CTD, [U-13C; U-15N], 1 mM; potassium phosphate 25 mM; potassium chloride 225 mM; TCEP 1 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.3; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCANH	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH TOCSY	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

ProcheckNMR, Laskowski and MacArthur - geometry optimization

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

PDB	2MAX
DBJ	BAJ55821 BAJ56204 BAJ58801 BAJ60323 BAM97153
EMBL	CAJ99012 CAX29978 CBI65743
GB	AAD06815 AAD08336 ABF85305 ACD48738 ACI27991
REF	NP_208085 WP_000864476 WP_000864477 WP_000864478 WP_000864479
SP	P56001 Q17ZB4 Q1CRW7 Q9ZJT5

Biological Magnetic Resonance Data Bank