BMRB Entry 15655

Name: Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34
Published: 2008-05-22

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PDB ID: 2k0q
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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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of CopK, a periplasmic protein involved in copper resistance in Cupriavidus metallidurans CH34

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:

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).
PubMed: 18533181

Assembly members:

Assembly members:
CopK, polymer, 74 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Cupriavidus metallidurans Taxonomy ID: 119219 Superkingdom: Bacteria Kingdom: not available Genus/species: Cupriavidus metallidurans

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET30

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CopK: VDMSNVVKTYDLQDGSKVHV FKDGKMGMENKFGKSMNMPE GKVMETRDGTKIIMKGNEIF RLDEALRKGHSEGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
H_exch_rates
- H_exch_rate_list_1
RDCs
- RDC_list_1

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
Samples and Experiments
Software
Spectrometers
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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

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

MET

LYS

GLY

ASN

GLU

ILE

PHE

7

ARG

LEU

ASP

GLU

ALA

LEU

ARG

LYS

GLY

HIS

8

SER

GLU

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

BMRB	16408 17716
PDB	2K0Q 2KM0 2LEL 3DSO 3DSP 3N7D 3N7E
EMBL	CAI11334
GB	ABF12967 EKZ95342
REF	WP_008652571 YP_145685
SP	Q58AD3
AlphaFold	Q58AD3