BMRB Entry 30756

Name: NMR structure of the putative GTPase-Activating (GAP) domain of VopE
Published: 2021-12-17

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PDB ID: 6x6n
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30756
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:

NMR structure of the putative GTPase-Activating (GAP) domain of VopE

Deposition date:

2020-05-28

Original release date:

2021-12-17

Authors:

Smith, K.; Lee, W.; Tonelli, M.

Citation:

Citation: Smith, Kyle; Lee, Woonghee; Tonelli, Marco; Lee, Yeongjoon; Light, Samuel; Cornilescu, Gabriel; Chakravarthy, Srinivas. "Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach" Protein Sci. 31, e4282-e4282 (2022).
PubMed: 35137487

Assembly members:

Assembly members:
entity_1, polymer, 134 residues, 14927.961 Da.

Natural source:

Natural source: Common Name: Vibrio cholerae Taxonomy ID: 666 Superkingdom: Bacteria Kingdom: not available Genus/species: Vibrio cholerae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPERISKAYESKDVRLVARD SAFLGLQRAIRSERFELDNF KSNFPYLTVANGSLRTIVTG LKGIVEFDDGQMKDIAKEIL DTQICGVPFSQFGTCSGSAR DLVDNASYQQEKIIIKHLNE LFEKVALHLVGAEV

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	447
15N chemical shifts	138
1H chemical shifts	931

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_1 134 residues - 14927.961 Da.

1

GLY

PRO

GLU

ARG

ILE

SER

LYS

ALA

TYR

GLU

2

SER

LYS

ASP

VAL

ARG

LEU

VAL

ALA

ARG

ASP

3

SER

ALA

PHE

LEU

GLY

LEU

GLN

ARG

ALA

ILE

4

ARG

SER

GLU

ARG

PHE

GLU

LEU

ASP

ASN

PHE

5

LYS

SER

ASN

PHE

PRO

TYR

LEU

THR

VAL

ALA

6

ASN

GLY

SER

LEU

ARG

THR

ILE

VAL

THR

GLY

7

LEU

LYS

GLY

ILE

VAL

GLU

PHE

ASP

GLY

8

GLN

MET

LYS

ASP

ILE

ALA

LYS

GLU

ILE

LEU

9

ASP

THR

GLN

ILE

CYS

GLY

VAL

PRO

PHE

SER

10

GLN

PHE

GLY

THR

CYS

SER

GLY

SER

ALA

ARG

11

ASP

LEU

VAL

ASP

ASN

ALA

SER

TYR

GLN

12

GLU

LYS

ILE

LYS

HIS

LEU

ASN

GLU

13

LEU

PHE

GLU

LYS

VAL

ALA

LEU

HIS

LEU

VAL

14

GLY

ALA

GLU

VAL

Samples:

sample_1: VopE GAP Domain, [U-13C; U-15N], 0.960 mM; HEPES pH 6.0 10 mM; sodium chloride 150 mM; TCEP 0.5 mM; D2O 10 v/v

sample_conditions_1: ionic strength: 150 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_1
3D HNCACB	sample_1	anisotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	anisotropic	sample_conditions_1
3D HNCO	sample_1	anisotropic	sample_conditions_1
3D C(CO)NH	sample_1	anisotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	anisotropic	sample_conditions_1
3D HCCH-COSY	sample_1	anisotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	anisotropic	sample_conditions_1
2D Aromatic 1H-13C HSQC	sample_1	anisotropic	sample_conditions_1
2D CBHD aromatic	sample_1	anisotropic	sample_conditions_1
2D ARTSY	sample_1	isotropic	sample_conditions_1
3D H(C)CH-TOCSY aromatic	sample_1	anisotropic	sample_conditions_1
2D CBHDHE aromatic	sample_1	anisotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	anisotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	anisotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	anisotropic	sample_conditions_1

Software:

VNMR v4.2, Varian - collection

TopSpin v3.5, Bruker Biospin - collection

NMRFAM-SPARKY, Woonghee Lee, Marco Tonelli, John L Markley - chemical shift assignment, peak picking

PONDEROSA-C/S, Woonghee Lee, Jaime L. Stark, John L. Markley - structure calculation

TALOS-N, Cornilescu, Delaglio and Bax - structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

PyMOL, Schroedinger - refinement

NMR spectrometers:

Agilent Varian VNMRS 600 MHz
Bruker AVANCE III 750 MHz

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