BMRB Entry 52646

Name: Complex DdvANt with DdvS sigma 4 domain
Published: 2025-01-09

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52646

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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:

Complex DdvANt with DdvS sigma 4 domain

Deposition date:

2024-10-21

Original release date:

2025-01-09

Authors:

Pantoja-Uceda, D.; Padmanabhan, S.

Citation:

Citation: Bernal-Bernal, Diego; Pantoja-Uceda, David; Lopez-Alonso, Jorge Pedro; Lopez-Rojo, Alfonso; Lopez-Ruiz, Jose Antonio; Galbis-Martinez, Marisa; Ochoa-Lizarralde, Borja; Tascon, Igor; Elias-Arnanz, Montserrat; Ubarretxena-Belandia, Iban; Padmanabhan, S.. "Structural basis for regulation of a CBASS-CRISPR-Cas defense island by a transmembrane anti-sigma factor and its ECF sigma partner" Sci. Adv. 10, eadp1053-eadp1053 (2024).
PubMed: 39454004

Assembly members:

Assembly members:
entity_1, polymer, 90 residues, 10068.254 Da.
entity_2, polymer, 90 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Myxococcus xanthus Taxonomy ID: 34 Superkingdom: Bacteria Kingdom: not available Genus/species: Myxococcus xanthus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pKT25

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSSHHHHHHSSGLVPRGSHM MSSSPCDQLQSFADGDLPPM EAQAFGQHLADCEKCQVELT RLLQLDQLGRGYIERHGPVD IPWHALPRNR
entity_2: GDPTITRWTLAQQGASGATY ERITEERFDWAIGKLPQQQR LTFLLRSQGLRNQEIALKLG VSPGTVAKRLFDARQRLSEL LKPYVDEGTH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	270
15N chemical shifts	71
1H chemical shifts	488

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	comp1	1
2	comp2	2
3	comp3	3

Entities:

Entity 1, comp1 90 residues - 10068.254 Da.

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

Entity 2, comp2 90 residues - Formula weight is not available

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

Entity 3, comp3 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: DdvANt, [U-13C; U-15N], 0.7 mM; sodium chloride 100 mM; TRIS 20 mM; beta-mercaptoethanol 2 mM; sodium azide 0.05%; DdvANt-DdvS_sigma4 0.7 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; 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_1	isotropic	sample_conditions_1
2D 1H-15N BEST TROSY	sample_1	isotropic	sample_conditions_1
3D HNCO BEST TROSY	sample_1	isotropic	sample_conditions_1
3D HNCA BEST TROSY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH BEST TROSY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN - collection, processing

NMRPipe - processing

NMRView - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker AVANCE NEO 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

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

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

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

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

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

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