BMRB Entry 19380

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19380
MolProbity Validation Chart

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Title:
NMR structure of the RNA polymerase alpha subunit C-terminal domain from Helicobacter pylori
Deposition date:
2013-07-21
Original release date:
2014-02-13
Authors:
Borin, Brendan; Krezel, Andrzej
Citation:

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).
PubMed: 24442709

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
13C chemical shifts340
15N chemical shifts112
1H chemical shifts736

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA polymerase alpha subunit C-terminal domain1

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   METARGGLYSERHISHISHISHISHISHIS
2   GLYSERLEUGLYVALPHEGLYGLUARGPRO
3   ILEALAASNTHRGLUTYRSERGLYASPTYR
4   ALAGLNARGASPASPALALYSASPLEUSER
5   ALALYSILEGLUSERMETASNLEUSERALA
6   ARGCYSPHEASNCYSLEUASPLYSILEGLY
7   ILELYSTYRVALGLYGLULEUVALLEUMET
8   SERGLUGLUGLULEULYSGLYVALLYSASN
9   METGLYLYSLYSSERTYRASPGLUILEALA
10   GLULYSLEUASNASPLEUGLYTYRPROVAL
11   GLYTHRGLULEUSERPROGLUGLNARGGLU
12   SERLEULYSLYSARGLEUGLULYSLEUGLU
13   ASPLYSGLYGLYASNASP

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCANHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HCCH TOCSYsample_2isotropicsample_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

Related Database Links:

PDB
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
AlphaFold Q17ZB4 P56001 Q1CRW7 Q9ZJT5

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