BMRB Entry 51674

Name: DinB-PAD
Published: 2023-06-23

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51674

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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:

DinB-PAD

Deposition date:

2022-10-28

Original release date:

2023-06-23

Authors:

Okeke, Damasus; Burmann, Bjorn

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, 124 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-SUMO

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GIDERDVNSERLRKSVGVER TMAEDIHHWSECEAIIERLY PELERRLAKVKPDLLIARQG VKLKFDDFQQTTQEHVWPRL NKADLIATARKTWDERRGGR GVRLVGLHVTLLDPQMERQL VLGL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	363
15N chemical shifts	118
1H chemical shifts	627

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DinB-PAd	1

Entities:

Entity 1, DinB-PAd 124 residues - Formula weight is not available

1

GLY

ILE

ASP

GLU

ARG

ASP

VAL

ASN

SER

GLU

2

ARG

LEU

ARG

LYS

SER

VAL

GLY

VAL

GLU

ARG

3

THR

MET

ALA

GLU

ASP

ILE

HIS

TRP

SER

4

GLU

CYS

GLU

ALA

ILE

GLU

ARG

LEU

TYR

5

PRO

GLU

LEU

GLU

ARG

LEU

ALA

LYS

VAL

6

LYS

PRO

ASP

LEU

ILE

ALA

ARG

GLN

GLY

7

VAL

LYS

LEU

LYS

PHE

ASP

PHE

GLN

8

THR

GLN

GLU

HIS

VAL

TRP

PRO

ARG

LEU

9

ASN

LYS

ALA

ASP

LEU

ILE

ALA

THR

ALA

ARG

10

LYS

THR

TRP

ASP

GLU

ARG

GLY

ARG

11

GLY

VAL

ARG

LEU

VAL

GLY

LEU

HIS

VAL

THR

12

LEU

ASP

PRO

GLN

MET

GLU

ARG

GLN

LEU

13

VAL

LEU

GLY

LEU

Samples:

sample_1: DinB-PAD, [U-100% 13C; U-100% 15N], 500 uM; KPi 50 mM; KCl 100 mM; Arginine 50 mM; Glutamine 50 mM; EDTA 1 mM; TCEP 1 mM; CHAPSO 0.1 mM; D2O 10%

sample_conditions_1: ionic strength: 200 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	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 HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3.6 - collection

NMRPipe - processing

CARA - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 700 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 900 MHz

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