BMRB Entry 16408

Name: Cu(I)-bound CopK
Published: 2010-03-12

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PDB ID: 2km0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16408
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Cu(I)-bound CopK

Deposition date:

2009-07-15

Original release date:

2010-03-12

Authors:

Bersch, Beate

Citation:

Citation: Sarret, Geraldine; Favier, Adrien; Coves, Jacques; Hazemann, Jean-Louis; Mergeay, Max; Bersch, Beate. "CopK from Cupriavidus metallidurans CH34 binds Cu(I) in a tetrathioether site: characterization by X-ray absorption and NMR spectroscopy." J. Am. Chem. Soc. 132, 3770-3777 (2010).
PubMed: 20192263

Assembly members:

Assembly members:
periplasmic CopK protein, polymer, 74 residues, 8294.617 Da.
CU1, non-polymer, 63.546 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available 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):
periplasmic CopK protein: VDMSNVVKTYDLQDGSKVHV FKDGKMGMENKFGKSMNMPE GKVMETRDGTKIIMKGNEIF RLDEALRKGHSEGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	278
15N chemical shifts	73
1H chemical shifts	496

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	CU1	2

Entities:

Entity 1, entity_1 74 residues - 8294.617 Da.

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

Entity 2, CU1 - Cu - 63.546 Da.

1

CU1

Samples:

sample_1: periplasmic CopK protein, [U-100% 15N], 1 mM; CU1 0.95 mM; ammonium acetate 50 mM; sodium ascorbate 10 mM

sample_2: periplasmic CopK protein, [U-100% 13C; U-100% 15N], 1.6 mM; CU1 1.5 mM; ammonium acetate 50 mM; sodium ascorbate 16 mM

sample_3: periplasmic CopK protein 1.5 mM; CU1 1.4 mM; ammonium acetate 50 mM; sodium ascorbate 14 mM

sample_conditions_1: pH: 6.8; pressure: 1.0 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment

ATHNOS-CANDID, Torsten Herrmann - peak picking, structure solution

ARIA v1.2, Linge, O'Donoghue and Nilges - structure solution

NMR spectrometers:

Varian DirectDrive 600 MHz
Varian DirectDrive 800 MHz

BMRB	15655 17716
PDB	2K0Q 2KM0 2LEL 3DSO 3DSP 3N7D 3N7E
EMBL	CAI11334
GB	ABF12967 EKZ95342
REF	WP_008652571 YP_145685
SP	Q58AD3
AlphaFold	Q58AD3