BMRB Entry 15896

Name: Solution structures of copper loaded form PCuA (trans conformation of the peptide bond involving the nitrogen of P14)
Published: 2008-11-14

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PDB ID: 2k6z
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/BMR15896
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structures of copper loaded form PCuA (trans conformation of the peptide bond involving the nitrogen of P14)

Deposition date:

2008-07-28

Original release date:

2008-11-14

Authors:

Banci, Lucia; Bertini, Ivano; Ciofi-Baffoni, Simone; Wang, Shenlin

Citation:

Citation: Abriata, Luciano; Banci, Lucia; Bertini, Ivano; Ciofi-Baffoni, Simone; Gkazonis, Petros; Spyroulias, Georgios; Vila, Alejandro; Wang, Shenlin. "Mechanism of Cu(A) assembly." Nat. Chemical Biol. 4, 599-601 (2008).
PubMed: 18758441

Assembly members:

Assembly members:
PCuA, polymer, 120 residues, 13222.670 Da.
CU, non-polymer, 63.546 Da.

Natural source:

Natural source: Common Name: Thermus thermophilus Taxonomy ID: 274 Superkingdom: Bacteria Kingdom: not available Genus/species: Thermus thermophilus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: BL21-Glod

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PCuA: GSFTEGWVRFSPGPNAAAYL TLENPGDLPLRLVGARTPVA ERVELHETFMREVEGKKVMG MRPVPFLEVPPKGRVELKPG GYHFMLLGLKRPLKAGEEVE LDLLFAGGKVLKVVLPVEAR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	505
15N chemical shifts	107
1H chemical shifts	844

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PCuA	1
2	COPPER (II) ION	2

Entities:

Entity 1, PCuA 120 residues - 13222.670 Da.

1	GLY	SER	PHE	THR	GLU	GLY	TRP	VAL	ARG	PHE
2	SER	PRO	GLY	PRO	ASN	ALA	ALA	ALA	TYR	LEU
3	THR	LEU	GLU	ASN	PRO	GLY	ASP	LEU	PRO	LEU
4	ARG	LEU	VAL	GLY	ALA	ARG	THR	PRO	VAL	ALA
5	GLU	ARG	VAL	GLU	LEU	HIS	GLU	THR	PHE	MET
6	ARG	GLU	VAL	GLU	GLY	LYS	LYS	VAL	MET	GLY
7	MET	ARG	PRO	VAL	PRO	PHE	LEU	GLU	VAL	PRO
8	PRO	LYS	GLY	ARG	VAL	GLU	LEU	LYS	PRO	GLY
9	GLY	TYR	HIS	PHE	MET	LEU	LEU	GLY	LEU	LYS
10	ARG	PRO	LEU	LYS	ALA	GLY	GLU	GLU	VAL	GLU
11	LEU	ASP	LEU	LEU	PHE	ALA	GLY	GLY	LYS	VAL
12	LEU	LYS	VAL	VAL	LEU	PRO	VAL	GLU	ALA	ARG

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

1

CU

Samples:

sample_1: entity_1, [U-100% 15N], 0.8 ± 0.1 mM; D2O, [U-99.9% 2H], 10%; H2O 90%; Pi 50 mM

sample_2: entity_1, [U-100% 13C; U-100% 15N], 0.8 ± 0.1 mM; D2O, [U-99.9% 2H], 10%; H2O 90%; Pi 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	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_1	isotropic	sample_conditions_1
15N R1	sample_1	isotropic	sample_conditions_1
15N R2	sample_1	isotropic	sample_conditions_1
1H-15N NOE	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, data analysis

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 500 MHz
Bruker Avance 400 MHz

BMRB	15894 15895 15897
PDB	2K6W 2K6Y 2K6Z 2K70
DBJ	BAD71766
GB	AAS81922 AEG34334 AFH39883
REF	WP_011173952 WP_011229034 WP_014510965 WP_014630387 YP_145209

1	GLY	SER	PHE	THR	GLU	GLY	TRP	VAL	ARG	PHE
2	SER	PRO	GLY	PRO	ASN	ALA	ALA	ALA	TYR	LEU
3	THR	LEU	GLU	ASN	PRO	GLY	ASP	LEU	PRO	LEU
4	ARG	LEU	VAL	GLY	ALA	ARG	THR	PRO	VAL	ALA
5	GLU	ARG	VAL	GLU	LEU	HIS	GLU	THR	PHE	MET
6	ARG	GLU	VAL	GLU	GLY	LYS	LYS	VAL	MET	GLY
7	MET	ARG	PRO	VAL	PRO	PHE	LEU	GLU	VAL	PRO
8	PRO	LYS	GLY	ARG	VAL	GLU	LEU	LYS	PRO	GLY
9	GLY	TYR	HIS	PHE	MET	LEU	LEU	GLY	LEU	LYS
10	ARG	PRO	LEU	LYS	ALA	GLY	GLU	GLU	VAL	GLU
11	LEU	ASP	LEU	LEU	PHE	ALA	GLY	GLY	LYS	VAL
12	LEU	LYS	VAL	VAL	LEU	PRO	VAL	GLU	ALA	ARG

1	GLY	SER	PHE	THR	GLU	GLY	TRP	VAL	ARG	PHE
2	SER	PRO	GLY	PRO	ASN	ALA	ALA	ALA	TYR	LEU
3	THR	LEU	GLU	ASN	PRO	GLY	ASP	LEU	PRO	LEU
4	ARG	LEU	VAL	GLY	ALA	ARG	THR	PRO	VAL	ALA
5	GLU	ARG	VAL	GLU	LEU	HIS	GLU	THR	PHE	MET
6	ARG	GLU	VAL	GLU	GLY	LYS	LYS	VAL	MET	GLY
7	MET	ARG	PRO	VAL	PRO	PHE	LEU	GLU	VAL	PRO
8	PRO	LYS	GLY	ARG	VAL	GLU	LEU	LYS	PRO	GLY
9	GLY	TYR	HIS	PHE	MET	LEU	LEU	GLY	LEU	LYS
10	ARG	PRO	LEU	LYS	ALA	GLY	GLU	GLU	VAL	GLU
11	LEU	ASP	LEU	LEU	PHE	ALA	GLY	GLY	LYS	VAL
12	LEU	LYS	VAL	VAL	LEU	PRO	VAL	GLU	ALA	ARG