BMRB Entry 18788
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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/BMR18788
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Title: Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+ PubMed: 23416741
Deposition date: 2012-10-14 Original release date: 2013-02-21
Authors: Xie, Tao; Feng, Yingang; Shan, Lu; Wang, Jinfeng
Citation: Xie, Tao; Feng, Yingang; Shan, Lu; Wang, Jinfeng. "Modeling of the [E43S]SNase-ssDNA-Cd(2+) complex: structural insight into the action of nuclease on ssDNA." Arch. Biochem. Biophys. 532, 103-113 (2013).
Assembly members:
staph_nuc_E43S, polymer, 149 residues, 16776.459 Da.
Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
staph_nuc_E43S: ATSTKKLHKEPATLIKAIDG
DTVKLMYKGQPMTFRLLLVD
TPSTKHPKKGVEKYGPEASA
FTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVN
EALVRQGLAKVAYVYKPNNT
HEQLLRKSEAQAKKEKLNIW
SEDNADSGQ
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 567 |
| 15N chemical shifts | 138 |
| 1H chemical shifts | 920 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | staph_nuc_E43S | 1 |
Entities:
Entity 1, staph_nuc_E43S 149 residues - 16776.459 Da.
| 1 | ALA | THR | SER | THR | LYS | LYS | LEU | HIS | LYS | GLU | ||||
| 2 | PRO | ALA | THR | LEU | ILE | LYS | ALA | ILE | ASP | GLY | ||||
| 3 | ASP | THR | VAL | LYS | LEU | MET | TYR | LYS | GLY | GLN | ||||
| 4 | PRO | MET | THR | PHE | ARG | LEU | LEU | LEU | VAL | ASP | ||||
| 5 | THR | PRO | SER | THR | LYS | HIS | PRO | LYS | LYS | GLY | ||||
| 6 | VAL | GLU | LYS | TYR | GLY | PRO | GLU | ALA | SER | ALA | ||||
| 7 | PHE | THR | LYS | LYS | MET | VAL | GLU | ASN | ALA | LYS | ||||
| 8 | LYS | ILE | GLU | VAL | GLU | PHE | ASP | LYS | GLY | GLN | ||||
| 9 | ARG | THR | ASP | LYS | TYR | GLY | ARG | GLY | LEU | ALA | ||||
| 10 | TYR | ILE | TYR | ALA | ASP | GLY | LYS | MET | VAL | ASN | ||||
| 11 | GLU | ALA | LEU | VAL | ARG | GLN | GLY | LEU | ALA | LYS | ||||
| 12 | VAL | ALA | TYR | VAL | TYR | LYS | PRO | ASN | ASN | THR | ||||
| 13 | HIS | GLU | GLN | LEU | LEU | ARG | LYS | SER | GLU | ALA | ||||
| 14 | GLN | ALA | LYS | LYS | GLU | LYS | LEU | ASN | ILE | TRP | ||||
| 15 | SER | GLU | ASP | ASN | ALA | ASP | SER | GLY | GLN |
Samples:
sample_1: staph_nuc_E43S, [U-13C; U-15N], 1.0 – 1.5 mM; sodium phosphate 50 mM; potassium chloride 150 mM; CdCl2 10 mM; sodium azide 0.2% w/v; 8-mer ssDNA(5, -CACTTCAT-3')', 2.25; 7, H2O, ; 8, D2O, ;
sample_conditions_1: ionic strength: 210 mM; pH: 6.6; pressure: 1 atm; temperature: 305 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHANH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
xwinnmr, Bruker Biospin - collection
FELIX, Accelrys Software Inc. - chemical shift assignment, data analysis, processing
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution
NMR spectrometers:
- Bruker DMX 600 MHz
Related Database Links:
| BMRB | 16585 1704 17718 18013 1874 1875 1876 1877 1878 4010 4052 4053 |
| PDB | |
| DBJ | BAB41979 BAB56977 BAB94634 BAF67032 BAF77694 |
| EMBL | CAA24594 CAG39855 CAG42530 CAI80436 CAQ49298 |
| GB | AAC14660 AAW36415 ABD22328 ABD29945 ABE02272 |
| PRF | 1109959A 710414A |
| REF | WP_000141556 WP_000141557 WP_001548082 WP_001566557 WP_001574556 |
| SP | P00644 Q5HHM4 Q6GB41 Q6GIK1 Q7A6P2 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts