BMRB Entry 26564

Name: Y-family polymerase Dbh (dinB homolog) from Sulfolobus acidocaldarius 1H, 15N, and 13C chemical shifts
Published: 2015-07-14

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26564

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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:

Y-family polymerase Dbh (dinB homolog) from Sulfolobus acidocaldarius 1H, 15N, and 13C chemical shifts

Deposition date:

2015-04-20

Original release date:

2015-07-14

Authors:

Moro, Sean; Cocco, Melanie

Citation:

Citation: Moro, Sean; Cocco, Melanie. "1H, 13C, and 15N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog" Biomol. NMR Assignments 9, 441-445 (2015).
PubMed: 26154586

Assembly members:

Assembly members:
Dbh_C31S, polymer, 360 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Sulfolobus acidocaldarius Taxonomy ID: 2285 Superkingdom: Archaea Kingdom: not available Genus/species: Sulfolobus acidocaldarius

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pKKT7-H

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dbh_C31S: MHHHHHHIVIFVDFDYFFAQ VEEVLNPQYKGKPLVVSVYS GRTKTSGAVATANYEARKLG VKAGMPIIKAMQIAPSAIYV PMRKPIYEAFSNRIMNLLNK HADKIEVASIDEAYLDVTNK VEGNFENGIELARKIKQEIL EKEKITVTVGVAPNKILAKI IADKSKPNGLGVIRPTEVQD FLNELDIDEIPGIGSVLARR LNELGIQKLRDILSKNYNEL EKITGKAKALYLLKLAQNKY SEPVENKSKIPHGRYLTLPY NTRDVKVILPYLKKAINEAY NKVNGIPMRITVIAIMEDLD ILSKGKKFKHGISIDNAYKV AEDLLRELLVRDKRRNVRRI GVKLDNIIINKTNLSDFFDI

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	1189
15N chemical shifts	568
1H chemical shifts	631

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DbhS C31S	1

Entities:

Entity 1, DbhS C31S 360 residues - Formula weight is not available

Residue 31 is Cys in WT Dbh Mutated to Ser.

1	MET	HIS	HIS	HIS	HIS	HIS	HIS	ILE	VAL	ILE
2	PHE	VAL	ASP	PHE	ASP	TYR	PHE	PHE	ALA	GLN
3	VAL	GLU	GLU	VAL	LEU	ASN	PRO	GLN	TYR	LYS
4	GLY	LYS	PRO	LEU	VAL	VAL	SER	VAL	TYR	SER
5	GLY	ARG	THR	LYS	THR	SER	GLY	ALA	VAL	ALA
6	THR	ALA	ASN	TYR	GLU	ALA	ARG	LYS	LEU	GLY
7	VAL	LYS	ALA	GLY	MET	PRO	ILE	ILE	LYS	ALA
8	MET	GLN	ILE	ALA	PRO	SER	ALA	ILE	TYR	VAL
9	PRO	MET	ARG	LYS	PRO	ILE	TYR	GLU	ALA	PHE
10	SER	ASN	ARG	ILE	MET	ASN	LEU	LEU	ASN	LYS
11	HIS	ALA	ASP	LYS	ILE	GLU	VAL	ALA	SER	ILE
12	ASP	GLU	ALA	TYR	LEU	ASP	VAL	THR	ASN	LYS
13	VAL	GLU	GLY	ASN	PHE	GLU	ASN	GLY	ILE	GLU
14	LEU	ALA	ARG	LYS	ILE	LYS	GLN	GLU	ILE	LEU
15	GLU	LYS	GLU	LYS	ILE	THR	VAL	THR	VAL	GLY
16	VAL	ALA	PRO	ASN	LYS	ILE	LEU	ALA	LYS	ILE
17	ILE	ALA	ASP	LYS	SER	LYS	PRO	ASN	GLY	LEU
18	GLY	VAL	ILE	ARG	PRO	THR	GLU	VAL	GLN	ASP
19	PHE	LEU	ASN	GLU	LEU	ASP	ILE	ASP	GLU	ILE
20	PRO	GLY	ILE	GLY	SER	VAL	LEU	ALA	ARG	ARG
21	LEU	ASN	GLU	LEU	GLY	ILE	GLN	LYS	LEU	ARG
22	ASP	ILE	LEU	SER	LYS	ASN	TYR	ASN	GLU	LEU
23	GLU	LYS	ILE	THR	GLY	LYS	ALA	LYS	ALA	LEU
24	TYR	LEU	LEU	LYS	LEU	ALA	GLN	ASN	LYS	TYR
25	SER	GLU	PRO	VAL	GLU	ASN	LYS	SER	LYS	ILE
26	PRO	HIS	GLY	ARG	TYR	LEU	THR	LEU	PRO	TYR
27	ASN	THR	ARG	ASP	VAL	LYS	VAL	ILE	LEU	PRO
28	TYR	LEU	LYS	LYS	ALA	ILE	ASN	GLU	ALA	TYR
29	ASN	LYS	VAL	ASN	GLY	ILE	PRO	MET	ARG	ILE
30	THR	VAL	ILE	ALA	ILE	MET	GLU	ASP	LEU	ASP
31	ILE	LEU	SER	LYS	GLY	LYS	LYS	PHE	LYS	HIS
32	GLY	ILE	SER	ILE	ASP	ASN	ALA	TYR	LYS	VAL
33	ALA	GLU	ASP	LEU	LEU	ARG	GLU	LEU	LEU	VAL
34	ARG	ASP	LYS	ARG	ARG	ASN	VAL	ARG	ARG	ILE
35	GLY	VAL	LYS	LEU	ASP	ASN	ILE	ILE	ILE	ASN
36	LYS	THR	ASN	LEU	SER	ASP	PHE	PHE	ASP	ILE

Samples:

15N_DbhS: Dbh C31S, [U-15N], 0.5 mM; D2O, [U-100% 2H], 10%

13C-15N-2H_DbhS: Dbh C31S, [U-100% 13C; U-100% 15N; U-80% 2H], 0.5 mM; D2O, [U-100% 2H], 10%

14N_Arg-_15N_DbhS: Dbh C31S, [U-15N; NA-Arg], 0.5 mM; D2O, [U-100% 2H], 10%

14N_Lys_15N_DbhS: Dbh C31S, [U-15N; NA-Lys], 0.5 mM; D2O, [U-100% 2H], 10%

14N_His_-_15N_DbhS: Dbh C31S, [U-15N; NA-His], 0.5 mM; D2O, [U-100% 2H], 10%

14N_Gly_15N_DbhS: Dbh C31S, [U-15N; NA-Gly], 0.5 mM; D2O, [U-100% 2H], 10%

14N_Asn_15N_DbhS: Dbh C31S, [U-15N; NA-Asn], 0.5 mM; D2O, [U-100% 2H], 10%

14N_Met_-_15N_DbhS: Dbh C31S, [U-15N; NA-Met], 0.5 mM; D2O, [U-100% 2H], 10%

15N_Asp_-_14N_DbhS: Dbh C31S, [U-15N-Asp], 0.5 mM; D2O, [U-100% 2H], 10%

14N_Arg_Asn_Gly_Ser_-_15N_DbhS: Dbh C31S, [U-15N; NA-Arg,Asn,Gly,Ser], 0.5 mM; D2O, [U-100% 2H], 10%

13CLeu_15N-2H_DbhS: Dbh C31S, [U-100% 13C-Leu; U-100% 15N; U-80% 2H], 0.5 mM; D2O, [U-100% 2H], 10%

35C: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 308 K

50C: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 323 K

45C: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 318 K

55C: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 328 K

65C: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 338 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N_DbhS	isotropic	35C
2D 1H-15N HSQC	15N_DbhS	isotropic	45C
2D 1H-15N HSQC	15N_DbhS	isotropic	50C
2D 1H-15N HSQC	15N_DbhS	isotropic	55C
2D 1H-15N HSQC	15N_DbhS	isotropic	65C
3D 1H-15N NOESY	15N_DbhS	isotropic	50C
3D HNCO	13C-15N-2H_DbhS	isotropic	50C
3D HNCACB	13C-15N-2H_DbhS	isotropic	50C
3D HN(CO)CA	13C-15N-2H_DbhS	isotropic	50C
3D HN(CA)CO	13C-15N-2H_DbhS	isotropic	50C
3D HNCA	13C-15N-2H_DbhS	isotropic	35C
3D HN(CO)CA	13C-15N-2H_DbhS	isotropic	35C
2D 1H-15N HSQC	14N_Lys_15N_DbhS	isotropic	45C
2D 1H-15N HSQC	14N_Lys_15N_DbhS	isotropic	55C
2D 1H-15N HSQC	14N_Arg-_15N_DbhS	isotropic	45C
2D 1H-15N HSQC	14N_Arg-_15N_DbhS	isotropic	55C
2D 1H-15N HSQC	14N_His_-_15N_DbhS	isotropic	35C
2D 1H-15N HSQC	14N_His_-_15N_DbhS	isotropic	55C
2D 1H-15N HSQC	14N_His_-_15N_DbhS	isotropic	45C
2D 1H-15N HSQC	15N_Asp_-_14N_DbhS	isotropic	50C
2D 1H-15N HSQC	14N_Met_-_15N_DbhS	isotropic	50C
2D 1H-15N HSQC	14N_Arg_Asn_Gly_Ser_-_15N_DbhS	isotropic	50C
2D 1H-15N HSQC	14N_Gly_15N_DbhS	isotropic	50C
2D 1H-15N HSQC	13C-15N-2H_DbhS	isotropic	35C
3D HNCO	13CLeu_15N-2H_DbhS	isotropic	50C

Software:

NMRPipe v7.8, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CCPNMR_Analysis v2.3.1, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

Varian INOVA 800 MHz

1	MET	HIS	HIS	HIS	HIS	HIS	HIS	ILE	VAL	ILE
2	PHE	VAL	ASP	PHE	ASP	TYR	PHE	PHE	ALA	GLN
3	VAL	GLU	GLU	VAL	LEU	ASN	PRO	GLN	TYR	LYS
4	GLY	LYS	PRO	LEU	VAL	VAL	SER	VAL	TYR	SER
5	GLY	ARG	THR	LYS	THR	SER	GLY	ALA	VAL	ALA
6	THR	ALA	ASN	TYR	GLU	ALA	ARG	LYS	LEU	GLY
7	VAL	LYS	ALA	GLY	MET	PRO	ILE	ILE	LYS	ALA
8	MET	GLN	ILE	ALA	PRO	SER	ALA	ILE	TYR	VAL
9	PRO	MET	ARG	LYS	PRO	ILE	TYR	GLU	ALA	PHE
10	SER	ASN	ARG	ILE	MET	ASN	LEU	LEU	ASN	LYS
11	HIS	ALA	ASP	LYS	ILE	GLU	VAL	ALA	SER	ILE
12	ASP	GLU	ALA	TYR	LEU	ASP	VAL	THR	ASN	LYS
13	VAL	GLU	GLY	ASN	PHE	GLU	ASN	GLY	ILE	GLU
14	LEU	ALA	ARG	LYS	ILE	LYS	GLN	GLU	ILE	LEU
15	GLU	LYS	GLU	LYS	ILE	THR	VAL	THR	VAL	GLY
16	VAL	ALA	PRO	ASN	LYS	ILE	LEU	ALA	LYS	ILE
17	ILE	ALA	ASP	LYS	SER	LYS	PRO	ASN	GLY	LEU
18	GLY	VAL	ILE	ARG	PRO	THR	GLU	VAL	GLN	ASP
19	PHE	LEU	ASN	GLU	LEU	ASP	ILE	ASP	GLU	ILE
20	PRO	GLY	ILE	GLY	SER	VAL	LEU	ALA	ARG	ARG
21	LEU	ASN	GLU	LEU	GLY	ILE	GLN	LYS	LEU	ARG
22	ASP	ILE	LEU	SER	LYS	ASN	TYR	ASN	GLU	LEU
23	GLU	LYS	ILE	THR	GLY	LYS	ALA	LYS	ALA	LEU
24	TYR	LEU	LEU	LYS	LEU	ALA	GLN	ASN	LYS	TYR
25	SER	GLU	PRO	VAL	GLU	ASN	LYS	SER	LYS	ILE
26	PRO	HIS	GLY	ARG	TYR	LEU	THR	LEU	PRO	TYR
27	ASN	THR	ARG	ASP	VAL	LYS	VAL	ILE	LEU	PRO
28	TYR	LEU	LYS	LYS	ALA	ILE	ASN	GLU	ALA	TYR
29	ASN	LYS	VAL	ASN	GLY	ILE	PRO	MET	ARG	ILE
30	THR	VAL	ILE	ALA	ILE	MET	GLU	ASP	LEU	ASP
31	ILE	LEU	SER	LYS	GLY	LYS	LYS	PHE	LYS	HIS
32	GLY	ILE	SER	ILE	ASP	ASN	ALA	TYR	LYS	VAL
33	ALA	GLU	ASP	LEU	LEU	ARG	GLU	LEU	LEU	VAL
34	ARG	ASP	LYS	ARG	ARG	ASN	VAL	ARG	ARG	ILE
35	GLY	VAL	LYS	LEU	ASP	ASN	ILE	ILE	ILE	ASN
36	LYS	THR	ASN	LEU	SER	ASP	PHE	PHE	ASP	ILE

1	MET	HIS	HIS	HIS	HIS	HIS	HIS	ILE	VAL	ILE
2	PHE	VAL	ASP	PHE	ASP	TYR	PHE	PHE	ALA	GLN
3	VAL	GLU	GLU	VAL	LEU	ASN	PRO	GLN	TYR	LYS
4	GLY	LYS	PRO	LEU	VAL	VAL	SER	VAL	TYR	SER
5	GLY	ARG	THR	LYS	THR	SER	GLY	ALA	VAL	ALA
6	THR	ALA	ASN	TYR	GLU	ALA	ARG	LYS	LEU	GLY
7	VAL	LYS	ALA	GLY	MET	PRO	ILE	ILE	LYS	ALA
8	MET	GLN	ILE	ALA	PRO	SER	ALA	ILE	TYR	VAL
9	PRO	MET	ARG	LYS	PRO	ILE	TYR	GLU	ALA	PHE
10	SER	ASN	ARG	ILE	MET	ASN	LEU	LEU	ASN	LYS
11	HIS	ALA	ASP	LYS	ILE	GLU	VAL	ALA	SER	ILE
12	ASP	GLU	ALA	TYR	LEU	ASP	VAL	THR	ASN	LYS
13	VAL	GLU	GLY	ASN	PHE	GLU	ASN	GLY	ILE	GLU
14	LEU	ALA	ARG	LYS	ILE	LYS	GLN	GLU	ILE	LEU
15	GLU	LYS	GLU	LYS	ILE	THR	VAL	THR	VAL	GLY
16	VAL	ALA	PRO	ASN	LYS	ILE	LEU	ALA	LYS	ILE
17	ILE	ALA	ASP	LYS	SER	LYS	PRO	ASN	GLY	LEU
18	GLY	VAL	ILE	ARG	PRO	THR	GLU	VAL	GLN	ASP
19	PHE	LEU	ASN	GLU	LEU	ASP	ILE	ASP	GLU	ILE
20	PRO	GLY	ILE	GLY	SER	VAL	LEU	ALA	ARG	ARG
21	LEU	ASN	GLU	LEU	GLY	ILE	GLN	LYS	LEU	ARG
22	ASP	ILE	LEU	SER	LYS	ASN	TYR	ASN	GLU	LEU
23	GLU	LYS	ILE	THR	GLY	LYS	ALA	LYS	ALA	LEU
24	TYR	LEU	LEU	LYS	LEU	ALA	GLN	ASN	LYS	TYR
25	SER	GLU	PRO	VAL	GLU	ASN	LYS	SER	LYS	ILE
26	PRO	HIS	GLY	ARG	TYR	LEU	THR	LEU	PRO	TYR
27	ASN	THR	ARG	ASP	VAL	LYS	VAL	ILE	LEU	PRO
28	TYR	LEU	LYS	LYS	ALA	ILE	ASN	GLU	ALA	TYR
29	ASN	LYS	VAL	ASN	GLY	ILE	PRO	MET	ARG	ILE
30	THR	VAL	ILE	ALA	ILE	MET	GLU	ASP	LEU	ASP
31	ILE	LEU	SER	LYS	GLY	LYS	LYS	PHE	LYS	HIS
32	GLY	ILE	SER	ILE	ASP	ASN	ALA	TYR	LYS	VAL
33	ALA	GLU	ASP	LEU	LEU	ARG	GLU	LEU	LEU	VAL
34	ARG	ASP	LYS	ARG	ARG	ASN	VAL	ARG	ARG	ILE
35	GLY	VAL	LYS	LEU	ASP	ASN	ILE	ILE	ILE	ASN
36	LYS	THR	ASN	LEU	SER	ASP	PHE	PHE	ASP	ILE