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
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Title: ArsR DNA Binding Domain PubMed: 19117956
Deposition date: 2008-06-11 Original release date: 2009-02-09
Authors: Gupta, Shobhana; Cover, Timothy; Krezel, Andrzej
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).
Assembly members:
ArsR, polymer, 115 residues, 13278 Da.
Natural source: Common Name: Helicobacter pylori 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):
ArsR: MRGSHHHHHHGSEEVSEPGD
ANIFRVDKDSREVYMHEKKL
DLTRAEYEILSLLISKKGYV
FSRESIAIESESINPESSNK
SIDVIIGRLRSKIEKNPKQP
QYIISVRGIGYKLEY
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 321 |
| 15N chemical shifts | 100 |
| 1H chemical shifts | 671 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | ArsR | 1 |
Entities:
Entity 1, ArsR 115 residues - 13278 Da.
Residues 1-12 in author's numbering are an added His tag.
| 1 | MET | ARG | GLY | SER | HIS | HIS | HIS | HIS | HIS | HIS | ||||
| 2 | GLY | SER | GLU | GLU | VAL | SER | GLU | PRO | GLY | ASP | ||||
| 3 | ALA | ASN | ILE | PHE | ARG | VAL | ASP | LYS | ASP | SER | ||||
| 4 | ARG | GLU | VAL | TYR | MET | HIS | GLU | LYS | LYS | LEU | ||||
| 5 | ASP | LEU | THR | ARG | ALA | GLU | TYR | GLU | ILE | LEU | ||||
| 6 | SER | LEU | LEU | ILE | SER | LYS | LYS | GLY | TYR | VAL | ||||
| 7 | PHE | SER | ARG | GLU | SER | ILE | ALA | ILE | GLU | SER | ||||
| 8 | GLU | SER | ILE | ASN | PRO | GLU | SER | SER | ASN | LYS | ||||
| 9 | SER | ILE | ASP | VAL | ILE | ILE | GLY | ARG | LEU | ARG | ||||
| 10 | SER | LYS | ILE | GLU | LYS | ASN | PRO | LYS | GLN | PRO | ||||
| 11 | GLN | TYR | ILE | ILE | SER | VAL | ARG | GLY | ILE | GLY | ||||
| 12 | TYR | LYS | LEU | GLU | TYR |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCANH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCC-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HHC-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CC)(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCC(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_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 simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts