BMRB Entry 17716

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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/BMR17716
MolProbity Validation Chart

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Title:
Structure of Cu(I)Cu(II)-CopK from Cupriavidus metallidurans CH34
Deposition date:
2011-06-16
Original release date:
2011-10-12
Authors:
Hinds, Mark; Xiao, Zhiguang; Chong, Lee Xin; Wedd, Anthony
Citation:

Citation: Ash, Miriam-Rose; Chong, Lee Xin; Maher, Megan; Hinds, Mark; Xiao, Zhiguang; Wedd, Anthony. "Molecular basis of the cooperative binding of Cu(I) and Cu(II) to the CopK protein from Cupriavidus metallidurans CH34."  Biochemistry 50, 9237-9247 (2011).
PubMed: 21936507

Assembly members:

Assembly members:
Cu(I)Cu(II)-CopK, polymer, 74 residues, 8294.617 Da.
CU1, non-polymer, 63.546 Da.
CU, non-polymer, 63.546 Da.
HOH, non-polymer, 18.015 Da.

Natural source:

Natural source:   Common Name: Cupriavidus metallidurans   Taxonomy ID: 266264   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Cupriavidus metallidurans

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pCX07

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Cu(I)Cu(II)-CopK: VDMSNVVKTYDLQDGSKVHV FKDGKMGMENKFGKSMNMPE GKVMETRDGTKIIMKGNEIF RLDEALRKGHSEGG

Data sets:
Data typeCount
13C chemical shifts252
15N chemical shifts68
1H chemical shifts400

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Cu(I)Cu(II)-CopK1
2COPPER (I) ION2
3CU23
4water4

Entities:

Entity 1, Cu(I)Cu(II)-CopK 74 residues - 8294.617 Da.

1-74 represent the processed form of the protein found in the periplasim

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

Entity 2, COPPER (I) ION - Cu - 63.546 Da.

1   CU1

Entity 3, CU2 - Cu - 63.546 Da.

1   CU

Entity 4, water - H2 O - 18.015 Da.

1   HOH

Samples:

sample_1: Cu(I)Cu(II)-CopK 1.5 mM; H2O 95%; D2O 5%

sample_2: Cu(I)Cu(II)-CopK, [U-100% 13C; U-100% 15N], 1.0 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 100 mM; pH: 6.7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2anisotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

XEASY, Bartels et al. - data analysis

TALOS, Cornilescu, Delaglio and Bax - processing

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

Related Database Links:

BMRB 15655 16408
PDB
EMBL CAI11334
GB ABF12967 EKZ95342
REF WP_008652571 YP_145685
SP Q58AD3
AlphaFold Q58AD3

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SPARKY: Backbone or all simulated peaks