BMRB Entry 11590
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11590
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: Solution Structure of the PhoP DNA-Binding Domain from Mycobacterium tuberculosis PubMed: 26209027
Deposition date: 2015-04-17 Original release date: 2015-08-10
Authors: Macdonald, Ramsay; Sarkar, Dibyendu; Amer, Brendan; Clubb, Robert
Citation: Macdonald, Ramsay; Sarkar, Dibyendu; Amer, Brendan; Clubb, Robert. "Solution structure of the PhoP DNA-binding domain from Mycobacterium tuberculosis" J. Biomol. NMR ., .-. (2015).
Assembly members:
PhoPC, polymer, 128 residues, 14723.858 Da.
Natural source: Common Name: Mycobacterium tuberculosis Taxonomy ID: 1773 Superkingdom: Bacteria Kingdom: not available Genus/species: Mycobacterium tuberculosis
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
PhoPC: MGSSHHHHHHSSGLVPRGSH
MKGNKEPRNVRLTFADIELD
EETHEVWKAGQPVSLSPTEF
TLLRYFVINAGTVLSKPKIL
DHVWRYDFGGDVNVVESYVS
YLRRKIDTGEKRLLHTLRGV
GYVLREPR
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 453 |
| 15N chemical shifts | 98 |
| 1H chemical shifts | 673 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | PhoP DNA-Binding Domain | 1 |
Entities:
Entity 1, PhoP DNA-Binding Domain 128 residues - 14723.858 Da.
Residues 120-141 represent a histidine-tag
| 1 | MET | GLY | SER | SER | HIS | HIS | HIS | HIS | HIS | HIS | ||||
| 2 | SER | SER | GLY | LEU | VAL | PRO | ARG | GLY | SER | HIS | ||||
| 3 | MET | LYS | GLY | ASN | LYS | GLU | PRO | ARG | ASN | VAL | ||||
| 4 | ARG | LEU | THR | PHE | ALA | ASP | ILE | GLU | LEU | ASP | ||||
| 5 | GLU | GLU | THR | HIS | GLU | VAL | TRP | LYS | ALA | GLY | ||||
| 6 | GLN | PRO | VAL | SER | LEU | SER | PRO | THR | GLU | PHE | ||||
| 7 | THR | LEU | LEU | ARG | TYR | PHE | VAL | ILE | ASN | ALA | ||||
| 8 | GLY | THR | VAL | LEU | SER | LYS | PRO | LYS | ILE | LEU | ||||
| 9 | ASP | HIS | VAL | TRP | ARG | TYR | ASP | PHE | GLY | GLY | ||||
| 10 | ASP | VAL | ASN | VAL | VAL | GLU | SER | TYR | VAL | SER | ||||
| 11 | TYR | LEU | ARG | ARG | LYS | ILE | ASP | THR | GLY | GLU | ||||
| 12 | LYS | ARG | LEU | LEU | HIS | THR | LEU | ARG | GLY | VAL | ||||
| 13 | GLY | TYR | VAL | LEU | ARG | GLU | PRO | ARG |
Samples:
sample_1: sodium phosphate 50.0 mM; sodium chloride 300.0 mM; sodium azide 0.01%; PhoPC, [U-100% 13C; U-100% 15N], 1.0 ± 0.5 mM; H2O 93%; D2O, [U-2H], 7%
sample_2: sodium phosphate 50.0 mM; sodium chloride 300.0 mM; sodium azide 0.01%; PhoPC, [U-100% 13C; U-100% 15N], 1.0 ± 0.5 mM; D2O, [U-2H], 100%
sample_conditions_1: ionic strength: 350 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHANH | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
Software:
X-PLOR_NIH v2.25, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
PIPP, Garrett - peak picking
TALOS, Cornilescu, Delaglio and Bax - dihedral angle calculation
ProcheckNMR, Laskowski and MacArthur - statistics
UNIO, Herrmann - data analysis, peak picking, structure solution
ATNOS-CANDID, Herrmann, Guntert and Wuthrich - data analysis, peak picking
CARA, Keller and Wuthrich - chemical shift assignment
NMR spectrometers:
- Bruker Avence 500 MHz
- Bruker Avence 600 MHz
- Bruker Avence 800 MHz
Related Database Links:
| PDB | |
| DBJ | BAH25072 BAL64650 BAQ04662 GAA44527 |
| EMBL | CAL70795 CCC25841 CCC43101 CCC63367 CCE36300 |
| GB | AAK45023 ABQ72495 ABR05115 ACT23809 AEB02905 |
| REF | NP_215271 NP_854438 WP_003403867 WP_003915456 WP_012054162 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts