BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15655

Title: Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34   PubMed: 18533181

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

Data sets:
Data typeCount
13C chemical shifts301
15N chemical shifts77
1H chemical shifts519
heteronuclear NOE values68
H exchange rates63
residual dipolar couplings133
T1 relaxation values62
T1rho relaxation values65
T2 relaxation values63

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1CopK_A1
2CopK_B1

Entities:

Entity 1, CopK_A 74 residues - Formula weight is not available

sequence of processed protein as recovered from E. coli periplasm

1   VALASPMETSERASNVALVALLYSTHRTYR
2   ASPLEUGLNASPGLYSERLYSVALHISVAL
3   PHELYSASPGLYLYSMETGLYMETGLUASN
4   LYSPHEGLYLYSSERMETASNMETPROGLU
5   GLYLYSVALMETGLUTHRARGASPGLYTHR
6   LYSILEILEMETLYSGLYASNGLUILEPHE
7   ARGLEUASPGLUALALEUARGLYSGLYHIS
8   SERGLUGLYGLY

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D HNCO-typesample_4anisotropicsample_conditions_1
relaxationsample_2isotropicsample_conditions_1
3D 15N NOESY-HSQCsample_2isotropicsample_conditions_1
2D-Sofastsample_2isotropicsample_conditions_1
relaxationsample_5isotropicsample_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 2K0Q 2KM0 2LEL 3DSO 3DSP 3N7D 3N7E
EMBL CAI11334
GB ABF12967 EKZ95342
REF WP_008652571 YP_145685 YP_581917
SP Q58AD3