BMRB Entry 25658

Name: NMR STRUCTURE OF A 180 RESIDUE CONSTRUCT ENCOMPASSING THE N- TERMINAL METAL-BINDING SITE AND THE MEMBRANE PROXIMAL DOMAIN OF SILB FROM CUPRIAVIDUS METALLIDURANS CH34
Published: 2016-05-23

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PDB ID: 5a4g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR25658
MolProbity Validation Chart

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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:

NMR STRUCTURE OF A 180 RESIDUE CONSTRUCT ENCOMPASSING THE N- TERMINAL METAL-BINDING SITE AND THE MEMBRANE PROXIMAL DOMAIN OF SILB FROM CUPRIAVIDUS METALLIDURANS CH34

Deposition date:

2015-06-10

Original release date:

2016-05-23

Authors:

Bersch, Beate; Urbina Fernandez, Patricia; Vandenbussche, Guy

Citation:

Citation: Urbina, Patricia; Bersch, Beate; De Angelis, Fabien; Derfoufi, Kheiro-Mouna; Prevost, Martine; Goormaghtigh, Erik; Vandenbussche, Guy. "Structural and Functional Investigation of the Ag(+)/Cu(+) Binding Domains of the Periplasmic Adaptor Protein SilB from Cupriavidus metallidurans CH34" Biochemistry 55, 2883-2897 (2016).
PubMed: 27145046

Assembly members:

Assembly members:
ag_silbnm2, polymer, 180 residues, 19044.5717 Da.

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: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ag_silbnm2: MGSATVNGPHDGHDPAAGAE LKTGKRILYWRDPMVPGQRF DKPGKSPYMDMPLIPVYEEE NADGAAVRIDGRVTQNLGVR TAEVKLGRLGSTERLLVPSE ALIRTGARTIAMVAKGEGGF DPVEVKAGATAGGQSEILEG LKAGQQVVVSGQFLIDSEAS LRGTVARMQETTSGLEVLFQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list
spectral_peak_list

Data type	Count
13C chemical shifts	678
15N chemical shifts	159
1H chemical shifts	970

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ag silbnm2, chain 1	1
2	ag silbnm2, chain 2	1

Entities:

Entity 1, ag silbnm2, chain 1 180 residues - 19044.5717 Da.

1	MET	GLY	SER	ALA	THR	VAL	ASN	GLY	PRO	HIS
2	ASP	GLY	HIS	ASP	PRO	ALA	ALA	GLY	ALA	GLU
3	LEU	LYS	THR	GLY	LYS	ARG	ILE	LEU	TYR	TRP
4	ARG	ASP	PRO	MET	VAL	PRO	GLY	GLN	ARG	PHE
5	ASP	LYS	PRO	GLY	LYS	SER	PRO	TYR	MET	ASP
6	MET	PRO	LEU	ILE	PRO	VAL	TYR	GLU	GLU	GLU
7	ASN	ALA	ASP	GLY	ALA	ALA	VAL	ARG	ILE	ASP
8	GLY	ARG	VAL	THR	GLN	ASN	LEU	GLY	VAL	ARG
9	THR	ALA	GLU	VAL	LYS	LEU	GLY	ARG	LEU	GLY
10	SER	THR	GLU	ARG	LEU	LEU	VAL	PRO	SER	GLU
11	ALA	LEU	ILE	ARG	THR	GLY	ALA	ARG	THR	ILE
12	ALA	MET	VAL	ALA	LYS	GLY	GLU	GLY	GLY	PHE
13	ASP	PRO	VAL	GLU	VAL	LYS	ALA	GLY	ALA	THR
14	ALA	GLY	GLY	GLN	SER	GLU	ILE	LEU	GLU	GLY
15	LEU	LYS	ALA	GLY	GLN	GLN	VAL	VAL	VAL	SER
16	GLY	GLN	PHE	LEU	ILE	ASP	SER	GLU	ALA	SER
17	LEU	ARG	GLY	THR	VAL	ALA	ARG	MET	GLN	GLU
18	THR	THR	SER	GLY	LEU	GLU	VAL	LEU	PHE	GLN

Samples:

13C-15N: ag_silbnm2, [U-99% 15N], 0.5 ± 0.05 mM; AgNO3 0.6 ± 0.06 mM; MES 50.0 ± 5 mM

sample_new_1: ag_silbnm2, [U-13C; U-15N], 0.5 ± 0.05 mM; AgNO3 0.6 ± 0.06 mM; MES 50 ± 5 mM

standard: ionic strength: 50 mM; pH: 6.300; pressure: 1.000 atm; temperature: 298.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC/HMQC	13C-15N	isotropic	standard
2D 1H-15N HSQC/HMQC	13C-15N	isotropic	standard
2D 1H-13C HSQC/HMQC	13C-15N	isotropic	standard
3D 1H-15N NOESY	13C-15N	isotropic	standard
3D 1H-13C NOESY	13C-15N	isotropic	standard
13C EDITED NOESY	sample_new_1	solution	standard
CNOESY-ATNOS	sample_new_1	solution	standard
13C EDITED NOESY	sample_new_1	solution	standard
AROMNOESY-ATNOS (CENTERED ON AROMATIC CARBONS)	sample_new_1	solution	standard
EXPT_13	sample_new_1	solution	standard
NNOESY_ATNOS	sample_new_1	solution	standard

Software:

Aria v2.3, Nilges - structure calculation

AutoDep v4.3, PDBe - chemical shift assignment

CNS v1.1, BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- - structure calculation

CcpNmr_Analysis v2.3, CCPN - assignment, spectrum analysis, spectrum display, structure calculation

cyana vany, Guntert, Mumenthaler and Wuthrich - structure calculation

nmrDraw vany, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - Spectrum display, processing

nmrPipe vany, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - Spectrum processing

nmrView vany, Johnson, One Moon Scientific - Spectrum analysis, Spectrum display

NMR spectrometers:

Bruker Avance II HD 850 MHz
Bruker Avance II HD 950 MHz
Bruker AVANCE 850 MHz
Bruker AVANCE 950 MHz

UniProt	Q58AF3_RALME
AlphaFold	Q58AF3

1	MET	GLY	SER	ALA	THR	VAL	ASN	GLY	PRO	HIS
2	ASP	GLY	HIS	ASP	PRO	ALA	ALA	GLY	ALA	GLU
3	LEU	LYS	THR	GLY	LYS	ARG	ILE	LEU	TYR	TRP
4	ARG	ASP	PRO	MET	VAL	PRO	GLY	GLN	ARG	PHE
5	ASP	LYS	PRO	GLY	LYS	SER	PRO	TYR	MET	ASP
6	MET	PRO	LEU	ILE	PRO	VAL	TYR	GLU	GLU	GLU
7	ASN	ALA	ASP	GLY	ALA	ALA	VAL	ARG	ILE	ASP
8	GLY	ARG	VAL	THR	GLN	ASN	LEU	GLY	VAL	ARG
9	THR	ALA	GLU	VAL	LYS	LEU	GLY	ARG	LEU	GLY
10	SER	THR	GLU	ARG	LEU	LEU	VAL	PRO	SER	GLU
11	ALA	LEU	ILE	ARG	THR	GLY	ALA	ARG	THR	ILE
12	ALA	MET	VAL	ALA	LYS	GLY	GLU	GLY	GLY	PHE
13	ASP	PRO	VAL	GLU	VAL	LYS	ALA	GLY	ALA	THR
14	ALA	GLY	GLY	GLN	SER	GLU	ILE	LEU	GLU	GLY
15	LEU	LYS	ALA	GLY	GLN	GLN	VAL	VAL	VAL	SER
16	GLY	GLN	PHE	LEU	ILE	ASP	SER	GLU	ALA	SER
17	LEU	ARG	GLY	THR	VAL	ALA	ARG	MET	GLN	GLU
18	THR	THR	SER	GLY	LEU	GLU	VAL	LEU	PHE	GLN

1	MET	GLY	SER	ALA	THR	VAL	ASN	GLY	PRO	HIS
2	ASP	GLY	HIS	ASP	PRO	ALA	ALA	GLY	ALA	GLU
3	LEU	LYS	THR	GLY	LYS	ARG	ILE	LEU	TYR	TRP
4	ARG	ASP	PRO	MET	VAL	PRO	GLY	GLN	ARG	PHE
5	ASP	LYS	PRO	GLY	LYS	SER	PRO	TYR	MET	ASP
6	MET	PRO	LEU	ILE	PRO	VAL	TYR	GLU	GLU	GLU
7	ASN	ALA	ASP	GLY	ALA	ALA	VAL	ARG	ILE	ASP
8	GLY	ARG	VAL	THR	GLN	ASN	LEU	GLY	VAL	ARG
9	THR	ALA	GLU	VAL	LYS	LEU	GLY	ARG	LEU	GLY
10	SER	THR	GLU	ARG	LEU	LEU	VAL	PRO	SER	GLU
11	ALA	LEU	ILE	ARG	THR	GLY	ALA	ARG	THR	ILE
12	ALA	MET	VAL	ALA	LYS	GLY	GLU	GLY	GLY	PHE
13	ASP	PRO	VAL	GLU	VAL	LYS	ALA	GLY	ALA	THR
14	ALA	GLY	GLY	GLN	SER	GLU	ILE	LEU	GLU	GLY
15	LEU	LYS	ALA	GLY	GLN	GLN	VAL	VAL	VAL	SER
16	GLY	GLN	PHE	LEU	ILE	ASP	SER	GLU	ALA	SER
17	LEU	ARG	GLY	THR	VAL	ALA	ARG	MET	GLN	GLU
18	THR	THR	SER	GLY	LEU	GLU	VAL	LEU	PHE	GLN