BMRB Entry 17283

Name: Sequence-specific 1H, 13C and 15N assignments of the phosphoesterase (PE) domain of Pseudomonas aeruginosa DNA ligase D (LigD)
Published: 2011-01-18

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PDB ID: 2lj6
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17283
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:

Sequence-specific 1H, 13C and 15N assignments of the phosphoesterase (PE) domain of Pseudomonas aeruginosa DNA ligase D (LigD)

Deposition date:

2010-11-03

Original release date:

2011-01-18

Authors:

Dutta, Kaushik; Natarajan, Aswin; Ghose, Ranajeet

Citation:

Citation: Dutta, Kaushik; Natarajan, Aswin; Nair, Pravin; Shuman, Stewart; Ghose, Ranajeet. "Sequence-specific 1H, 13C and 15N assignments of the phosphoesterase (PE) domain of Pseudomonas aeruginosa DNA ligase D (LigD)." Biomol. NMR Assignments 5, 151-155 (2011).
PubMed: 21213076

Assembly members:

Assembly members:
Pae177, polymer, 177 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Pseudomonas aeruginosa Taxonomy ID: 287 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas aeruginosa

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Pae177: MPSSKPLAEYARKRDFRQTP EPSGRKPRKDSTGLLRYCVQ KHDASRLHYDFRLELDGTLK SWAVPKGPCLDPAVKRLAVQ VEDHPLDYADFEGSIPQGHY GAGDVIVWDRGAWTPLDDPR EGLEKGHLSFALDGEKLSGR WHLIRTNLRGKQSQWFLVKA KDGEARSLDRFDVLKER

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	580
15N chemical shifts	150
1H chemical shifts	840

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Pae177	1

Entities:

Entity 1, Pae177 177 residues - Formula weight is not available

1

MET

PRO

SER

LYS

PRO

LEU

ALA

GLU

TYR

2

ALA

ARG

LYS

ARG

ASP

PHE

ARG

GLN

THR

PRO

3

GLU

PRO

SER

GLY

ARG

LYS

PRO

ARG

LYS

ASP

4

SER

THR

GLY

LEU

ARG

TYR

CYS

VAL

GLN

5

LYS

HIS

ASP

ALA

SER

ARG

LEU

HIS

TYR

ASP

6

PHE

ARG

LEU

GLU

LEU

ASP

GLY

THR

LEU

LYS

7

SER

TRP

ALA

VAL

PRO

LYS

GLY

PRO

CYS

LEU

8

ASP

PRO

ALA

VAL

LYS

ARG

LEU

ALA

VAL

GLN

9

VAL

GLU

ASP

HIS

PRO

LEU

ASP

TYR

ALA

ASP

10

PHE

GLU

GLY

SER

ILE

PRO

GLN

GLY

HIS

TYR

11

GLY

ALA

GLY

ASP

VAL

ILE

VAL

TRP

ASP

ARG

12

GLY

ALA

TRP

THR

PRO

LEU

ASP

PRO

ARG

13

GLU

GLY

LEU

GLU

LYS

GLY

HIS

LEU

SER

PHE

14

ALA

LEU

ASP

GLY

GLU

LYS

LEU

SER

GLY

ARG

15

TRP

HIS

LEU

ILE

ARG

THR

ASN

LEU

ARG

GLY

16

LYS

GLN

SER

GLN

TRP

PHE

LEU

VAL

LYS

ALA

17

LYS

ASP

GLY

GLU

ALA

ARG

SER

LEU

ASP

ARG

18

PHE

ASP

VAL

LEU

LYS

GLU

ARG

Samples:

NMR_Sample_1: Pae177, [U-100% 15N], 300 uM; D20 10%; H20 90%; Bis-Tris 50 mM; NaCl 200 mM; DTT 5 mM

NMR_Sample_2: Pae177, [U-100% 13C; U-100% 15N], 300 uM; D20 10%; H20 90%; Bis-Tris 50 mM; NaCl 200 mM; DTT 5 mM

NMR_Sample_3: Pae177, [U-13C; U-15N; U-2H], 300 uM; D20 10%; H20 90%; Bis-Tris 50 mM; NaCl 200 mM; DTT 5 mM

NMR: ionic strength: 200 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NMR_Sample_1	isotropic	NMR
2D 1H-15N HSQC	NMR_Sample_2	isotropic	NMR
2D 1H-15N HSQC	NMR_Sample_3	isotropic	NMR
3D HN(COCA)CB	NMR_Sample_1	isotropic	NMR
3D HNCACB	NMR_Sample_3	isotropic	NMR
3D C(CO)NH	NMR_Sample_1	isotropic	NMR
3D H(CCO)NH	NMR_Sample_1	isotropic	NMR
3D HNCO	NMR_Sample_3	isotropic	NMR
3D HNCA	NMR_Sample_3	isotropic	NMR
3D TROSY	NMR_Sample_3	isotropic	NMR
3D HNCOCACB	NMR_Sample_3	isotropic	NMR
3D HNCOCA	NMR_Sample_3	isotropic	NMR
3D HNCACO	NMR_Sample_3	isotropic	NMR
3D CC(CO)NH	NMR_Sample_2	isotropic	NMR
3D HC(CO)NH	NMR_Sample_2	isotropic	NMR
3D HBHACONH	NMR_Sample_2	isotropic	NMR

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 800 MHz
Bruker Avance 700 MHz
Varian INOVA 600 MHz

PDB	2LJ6 3N9B 3N9D
DBJ	BAK89966 BAP23425 BAP51031 BAQ40184 BAR68071
EMBL	CAW27916 CDH77490 CDM46092 CDO81319 CEI20600
GB	AAG05526 ABJ11315 AEO75385 AFM65275 AGI81805
REF	NP_250828 WP_003109866 WP_003113639 WP_003124692 WP_003158695
SP	Q9I1X7
AlphaFold	Q9I1X7