BMRB Entry 30985

Name: Solution structure of the phosphatidylinositol 3-phosphate binding domain from the Legionella effector SetA
Published: 2023-01-31

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PDB ID: 7tod
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30985
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:

Solution structure of the phosphatidylinositol 3-phosphate binding domain from the Legionella effector SetA

Deposition date:

2022-01-24

Original release date:

2023-01-31

Authors:

Beck, W.; Enoki, T.; Feigenson, G.; Nicholson, L.; Oswald, R.; Mao, Y.

Citation:

Citation: Beck, W.; Enoki, T.; Feigenson, G.; Nicholson, L.; Oswald, R.; Mao, Y.. "Solution structure of the phosphatidylinositol 3-phosphate binding domain from the Legionella effector SetA" .

Assembly members:

Assembly members:
entity_1, polymer, 108 residues, 12192.811 Da.

Natural source:

Natural source: Common Name: Legionella pneumophila Taxonomy ID: 446 Superkingdom: Bacteria Kingdom: not available Genus/species: Legionella pneumophila

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SDEKIKTAHDLIDEIIQDVI QLDGKLGLLGGNTRQLEDGR VINIPNGAAMIFDDYKKYKQ GELTAESALESMIKIAKLSN QLNRHTFFNQRQPETGQFYK KVAAIDLQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	467
15N chemical shifts	122
1H chemical shifts	797

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 108 residues - 12192.811 Da.

1

SER

ASP

GLU

LYS

ILE

LYS

THR

ALA

HIS

ASP

2

LEU

ILE

ASP

GLU

ILE

GLN

ASP

VAL

ILE

3

GLN

LEU

ASP

GLY

LYS

LEU

GLY

LEU

GLY

4

GLY

ASN

THR

ARG

GLN

LEU

GLU

ASP

GLY

ARG

5

VAL

ILE

ASN

ILE

PRO

ASN

GLY

ALA

MET

6

ILE

PHE

ASP

TYR

LYS

TYR

LYS

GLN

7

GLY

GLU

LEU

THR

ALA

GLU

SER

ALA

LEU

GLU

8

SER

MET

ILE

LYS

ILE

ALA

LYS

LEU

SER

ASN

9

GLN

LEU

ASN

ARG

HIS

THR

PHE

ASN

GLN

10

ARG

GLN

PRO

GLU

THR

GLY

GLN

PHE

TYR

LYS

11

LYS

VAL

ALA

ILE

ASP

LEU

GLN

Samples:

sample_1: protein, [U-100% 13C; U-100% 15N; U-80% 2H], 6 ± 0.3 mg/mL; sodium phosphate buffer 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.0; 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
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N-NOESYHSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C-NOESYHSQC (aromatic)	sample_1	isotropic	sample_conditions_1
3D 1H-13C-NOESYHSQC (aliphatic)	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PONDEROSA-C/S, Woonghee Lee - refinement, structure calculation

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Varian INOVA 500 MHz

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