BMRB Entry 51676

Name: DinBdeltaPAD
Published: 2023-06-23

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51676

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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:

DinBdeltaPAD

Deposition date:

2022-10-28

Original release date:

2023-06-23

Authors:

Burmann, Bjorn; Okeke, Damasus

Citation:

Citation: Okeke, Damasus; Lidman, Jens; Matecko-Burmann, Irena; Burmann, Bjorn. "Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)" Nucleic Acids Res. 51, 7036-7052 (2023).
PubMed: 37260088

Assembly members:

Assembly members:
entity_1, polymer, 250 residues, Formula weight is not available

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MGSSHHHHHHSSGLVPRGSH MRKIIHVDMDCFFAAVEMRD NPALRDIPIAIGGSRERRGV ISTANYPARKFGVRSAMPTG MALKLCPHLTLLPGRFDAYK EASNHIREIFSRYTSRIEPL SLDEAYLDVTDSVHCHGSAT LIAQEIRQTIFNELQLTASA GVAPVKFLAKIASDMNKPNG QFVITPAEVPAFLQTLPLAK IPGVGKVSAAKLEAMGLRTC GDVQKCDLVMLLKRFGKFGR ILWERSQGID

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	768
15N chemical shifts	209
1H chemical shifts	585

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DinBdeltaPAD	1

Entities:

Entity 1, DinBdeltaPAD 250 residues - Formula weight is not available

Includes N-terminal hexa-histidine tag

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

Samples:

sample_1: DinBdeltaPAD, [U-100% 13C; U-100% 15N; U-100% 2H], 275 uM; Arginine 50 mM; Glutamine 50 mM; EDTA 1 mM; TCEP 1 mM; CHAPSO 0.1 mM; D2O 10%

sample_2: DinBdeltaPAD, [U-100% 13C; U-100% 15N], 275 uM; Arginine 50 mM; Glutamine 50 mM; EDTA 1 mM; TCEP 1 mM; CHAPSO 0.1 mM; D2O 10%

sample_conditions_1: ionic strength: 250 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN - collection

NMRPipe - processing

CARA - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 700 MHz
Bruker AVANCE III 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	MET	GLY	SER	SER	HIS	HIS	HIS	HIS	HIS	HIS
2	SER	SER	GLY	LEU	VAL	PRO	ARG	GLY	SER	HIS
3	MET	ARG	LYS	ILE	ILE	HIS	VAL	ASP	MET	ASP
4	CYS	PHE	PHE	ALA	ALA	VAL	GLU	MET	ARG	ASP
5	ASN	PRO	ALA	LEU	ARG	ASP	ILE	PRO	ILE	ALA
6	ILE	GLY	GLY	SER	ARG	GLU	ARG	ARG	GLY	VAL
7	ILE	SER	THR	ALA	ASN	TYR	PRO	ALA	ARG	LYS
8	PHE	GLY	VAL	ARG	SER	ALA	MET	PRO	THR	GLY
9	MET	ALA	LEU	LYS	LEU	CYS	PRO	HIS	LEU	THR
10	LEU	LEU	PRO	GLY	ARG	PHE	ASP	ALA	TYR	LYS
11	GLU	ALA	SER	ASN	HIS	ILE	ARG	GLU	ILE	PHE
12	SER	ARG	TYR	THR	SER	ARG	ILE	GLU	PRO	LEU
13	SER	LEU	ASP	GLU	ALA	TYR	LEU	ASP	VAL	THR
14	ASP	SER	VAL	HIS	CYS	HIS	GLY	SER	ALA	THR
15	LEU	ILE	ALA	GLN	GLU	ILE	ARG	GLN	THR	ILE
16	PHE	ASN	GLU	LEU	GLN	LEU	THR	ALA	SER	ALA
17	GLY	VAL	ALA	PRO	VAL	LYS	PHE	LEU	ALA	LYS
18	ILE	ALA	SER	ASP	MET	ASN	LYS	PRO	ASN	GLY
19	GLN	PHE	VAL	ILE	THR	PRO	ALA	GLU	VAL	PRO
20	ALA	PHE	LEU	GLN	THR	LEU	PRO	LEU	ALA	LYS
21	ILE	PRO	GLY	VAL	GLY	LYS	VAL	SER	ALA	ALA
22	LYS	LEU	GLU	ALA	MET	GLY	LEU	ARG	THR	CYS
23	GLY	ASP	VAL	GLN	LYS	CYS	ASP	LEU	VAL	MET
24	LEU	LEU	LYS	ARG	PHE	GLY	LYS	PHE	GLY	ARG
25	ILE	LEU	TRP	GLU	ARG	SER	GLN	GLY	ILE	ASP

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

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