BMRB Entry 15655
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15655
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Title: Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34 PubMed: 18533181
Deposition date: 2008-02-12 Original release date: 2008-05-22
Authors: Bersch, Beate; Favier, Adrien; Schanda, Paul; Coves, Jacques; van Aelst, Sebastien; Vallaeys, Tatiana; Wattiez, Ruddy; Mergeay, Max
Citation: Bersch, Beate; Favier, Adrien; Schanda, Paul; van Aelst, Sebastien; Vallaeys, Tatiana; Coves, Jacques; Mergeay, Max; Wattiez, Ruddy. "Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge" J. Mol. Biol. 380, 386-403 (2008).
Assembly members:
CopK, polymer, 74 residues, Formula weight is not available
Natural source: Common Name: Cupriavidus metallidurans Taxonomy ID: 119219 Superkingdom: Bacteria Kingdom: not available Genus/species: Cupriavidus metallidurans
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
CopK: VDMSNVVKTYDLQDGSKVHV
FKDGKMGMENKFGKSMNMPE
GKVMETRDGTKIIMKGNEIF
RLDEALRKGHSEGG
- assigned_chemical_shifts
- heteronucl_NOEs
- heteronucl_T1_relaxation
- heteronucl_T2_relaxation
- H_exch_rates
- RDCs
| Data type | Count |
| 13C chemical shifts | 301 |
| 15N chemical shifts | 77 |
| 1H chemical shifts | 519 |
| heteronuclear NOE values | 68 |
| H exchange rates | 63 |
| residual dipolar couplings | 133 |
| T1 relaxation values | 62 |
| T1rho relaxation values | 65 |
| T2 relaxation values | 63 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | CopK_A | 1 |
| 2 | CopK_B | 1 |
Entities:
Entity 1, CopK_A 74 residues - Formula weight is not available
sequence of processed protein as recovered from E. coli periplasm
| 1 | VAL | ASP | MET | SER | ASN | VAL | VAL | LYS | THR | TYR | ||||
| 2 | ASP | LEU | GLN | ASP | GLY | SER | LYS | VAL | HIS | VAL | ||||
| 3 | PHE | LYS | ASP | GLY | LYS | MET | GLY | MET | GLU | ASN | ||||
| 4 | LYS | PHE | GLY | LYS | SER | MET | ASN | MET | PRO | GLU | ||||
| 5 | GLY | LYS | VAL | MET | GLU | THR | ARG | ASP | GLY | THR | ||||
| 6 | LYS | ILE | ILE | MET | LYS | GLY | ASN | GLU | ILE | PHE | ||||
| 7 | ARG | LEU | ASP | GLU | ALA | LEU | ARG | LYS | GLY | HIS | ||||
| 8 | SER | GLU | GLY | GLY |
Samples:
sample_1: CopK, [U-100% 13C; U-100% 15N], 1.5 ± 0.2 mM; H2O 90%; D2O 10%; MES 50 mM
sample_2: CopK, [U-100% 15N], 1.5 ± 0.2 mM; H2O 90%; D2O 10%; MES 50 mM
sample_4: CopK 1.5 ± 0.2 mM; H2O 90%; D2O 10%; MES 50 mM; C12E5 5%; hexanol 5%
sample_3: CopK 1.5 ± 0.2 mM; H2O 90%; D2O 10%; MES 50 mM
sample_5: CopK, [U-100% 15N], 0.5 ± 0.05 mM; H2O 90%; D2O 10%; MES 50 mM
sample_conditions_1: ionic strength: 0.1 M; pH: 6.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCO-type | sample_4 | anisotropic | sample_conditions_1 |
| relaxation | sample_2 | isotropic | sample_conditions_1 |
| 3D 15N NOESY-HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D-Sofast | sample_2 | isotropic | sample_conditions_1 |
| relaxation | sample_5 | isotropic | sample_conditions_1 |
Software:
VNMRJ, Varian - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - geometry optimization, peak picking
TALOS, Cornilescu, Delaglio and Bax - data analysis
Tensor, Dosset, Blackledge - data analysis
Module, Dosset, Blackledge - data analysis
NMR spectrometers:
- Varian INOVA 600 MHz
- Varian DirectDrive 600 MHz
- Varian INOVA 800 MHz
Related Database Links:
| BMRB | 16408 17716 |
| PDB | |
| EMBL | CAI11334 |
| GB | ABF12967 EKZ95342 |
| REF | WP_008652571 YP_145685 |
| SP | Q58AD3 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts