BMRB Entry 15801

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15801
MolProbity Validation Chart

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Title:
ArsR DNA Binding Domain
Deposition date:
2008-06-11
Original release date:
2009-02-09
Authors:
Gupta, Shobhana; Cover, Timothy; Krezel, Andrzej
Citation:

Citation: Gupta, Shobhana; Borin, Brendan; Cover, Timothy; Krezel, Andrzej. "Structural analysis of the DNA-binding domain of the Helicobacter pylori response regulator ArsR."  J. Biol. Chem. 284, 6536-6545 (2009).
PubMed: 19117956

Assembly members:

Assembly members:
ArsR, polymer, 115 residues, 13278 Da.

Natural source:

Natural source:   Common Name: Helicobacter pylori   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: pET-BNK

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ArsR: MRGSHHHHHHGSEEVSEPGD ANIFRVDKDSREVYMHEKKL DLTRAEYEILSLLISKKGYV FSRESIAIESESINPESSNK SIDVIIGRLRSKIEKNPKQP QYIISVRGIGYKLEY

Data sets:
Data typeCount
13C chemical shifts321
15N chemical shifts100
1H chemical shifts671

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1ArsR1

Entities:

Entity 1, ArsR 115 residues - 13278 Da.

Residues 1-12 in author's numbering are an added His tag.

1   METARGGLYSERHISHISHISHISHISHIS
2   GLYSERGLUGLUVALSERGLUPROGLYASP
3   ALAASNILEPHEARGVALASPLYSASPSER
4   ARGGLUVALTYRMETHISGLULYSLYSLEU
5   ASPLEUTHRARGALAGLUTYRGLUILELEU
6   SERLEULEUILESERLYSLYSGLYTYRVAL
7   PHESERARGGLUSERILEALAILEGLUSER
8   GLUSERILEASNPROGLUSERSERASNLYS
9   SERILEASPVALILEILEGLYARGLEUARG
10   SERLYSILEGLULYSASNPROLYSGLNPRO
11   GLNTYRILEILESERVALARGGLYILEGLY
12   TYRLYSLEUGLUTYR

Samples:

sample_1: entity, [U-100% 13C; U-100% 15N], 0.5 mM; NaCl 0.5 M

sample_conditions_1: ionic strength: 0.56 M; pH: 7.6; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D HCC-TOCSYsample_1isotropicsample_conditions_1
3D HHC-TOCSYsample_1isotropicsample_conditions_1
3D H(CC)(CO)NHsample_1isotropicsample_conditions_1
3D HCC(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - geometry optimization

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

CSI v2.0, Wishart, DS and Sykes, BD - data analysis

Molmol v2K.2, Koradi, Billeter and Wuthrich - structure visualization

ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis

Procheck v3.5.4, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho - data analysis

TOPSPIN v2.0, Bruker Biospin - processing

SPARKY v3.114, Goddard - chemical shift assignment, peak picking, processing

InsightII vv2005.03, Accelrys Software Inc. - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAJ54770 BAJ57228 BAJ57755 BAM96080 BAO97793
EMBL CAX28715 CBI66957
GB AAD05721 AAD07234 ABF84229 ACD47627 ACI26919
REF NP_206965 WP_000573695 WP_000573696 WP_000573697 WP_000573698

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