BMRB Entry 16238

Name: Solution NMR structure of VC_A0919 from Vibrio cholerae. Northeast Structural Genomics Consortium Target VcR52.
Published: 2009-05-07

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PDB ID: 2khd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16238
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of VC_A0919 from Vibrio cholerae. Northeast Structural Genomics Consortium Target VcR52.

Deposition date:

2009-04-02

Original release date:

2009-05-07

Authors:

Ramelot, Theresa; Cort, John; Wang, Huang; Ciccosanti, Colleen; Jiang, Mei; Liu, Jinfeng; Rost, Burkhard; Swapna, G.V.T.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Ramelot, Theresa; Cort, John; Wang, Huang; Ciccosanti, Colleen; Jiang, Mei; Liu, Jinfeng; Rost, Burkhard; Swapna, G.V.T.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of VC_A0919 from Vibrio cholerae. Northeast Structural Genomics Consortium Target VcR52." .

Assembly members:

Assembly members:
VC_A0919, polymer, 108 residues, 12000 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 Vector: pET21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VC_A0919: MSNQTCVENEVCEACGCAGE IGFIIREGDDVAEVSLFGSD KAHLEGKLAEYISLAKQVYA NVEYEVAPVADNATELHARF KFEVSAEKLIFELKTRALAR LEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	437
15N chemical shifts	102
1H chemical shifts	692

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VC_A0919	1

Entities:

Entity 1, VC_A0919 108 residues - 12000 Da.

8 non-native residues at C-teriminus (LEHHHHHH)

1

MET

SER

ASN

GLN

THR

CYS

VAL

GLU

ASN

GLU

2

VAL

CYS

GLU

ALA

CYS

GLY

CYS

ALA

GLY

GLU

3

ILE

GLY

PHE

ILE

ARG

GLU

GLY

ASP

4

VAL

ALA

GLU

VAL

SER

LEU

PHE

GLY

SER

ASP

5

LYS

ALA

HIS

LEU

GLU

GLY

LYS

LEU

ALA

GLU

6

TYR

ILE

SER

LEU

ALA

LYS

GLN

VAL

TYR

ALA

7

ASN

VAL

GLU

TYR

GLU

VAL

ALA

PRO

VAL

ALA

8

ASP

ASN

ALA

THR

GLU

LEU

HIS

ALA

ARG

PHE

9

LYS

PHE

GLU

VAL

SER

ALA

GLU

LYS

LEU

ILE

10

PHE

GLU

LEU

LYS

THR

ARG

ALA

LEU

ALA

ARG

11

LEU

GLU

HIS

Samples:

NC_sample: MES 20 ± 1 mM; sodium chloride 100 ± 10 mM; calcium chloride 5 ± 0.25 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 mM; protein, [U-100% 13C; U-100% 15N], 0.5 ± 0.05 mM

NC5_sample: MES 20 ± 1 mM; sodium chloride 100 ± 10 mM; calcium chloride 5 ± 0.25 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 mM; protein, [U-5% 13C; U-100% 15N], 0.5 ± 0.05 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC_sample	isotropic	sample_conditions_1
3D 1H-15N NOESY	NC_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY (aliph)	NC_sample	isotropic	sample_conditions_1
3D HNCO	NC_sample	isotropic	sample_conditions_1
3D HNCA	NC_sample	isotropic	sample_conditions_1
3D HN(CO)CA	NC_sample	isotropic	sample_conditions_1
3D CBCA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HNCACB	NC_sample	isotropic	sample_conditions_1
3D C(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HBHA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	NC_sample	isotropic	sample_conditions_1
3D HCCH-COSY	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC (aliph)	NC5_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY (arom)	NC_sample	isotropic	sample_conditions_1

Software:

NMRPipe v2008, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMR v6.1C, Varian - collection

TOPSPIN v2.1.3, Bruker Biospin - collection

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - data analysis

X-PLOR NIH v2.20, Schwieters, Kuszewski, Tjandra and Clore - structure solution

SPARKY v3.113, Goddard - data analysis

PSVS v1.3, Bhattacharya and Montelione - structure validation

AutoAssign v2.3.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

PDBStat v5.0, (PDBStat) R. Tejero, G.T. Montelione - data analysis

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz
Bruker AvanceIII 850 MHz

PDB	2KHD
DBJ	BAP05215
EMBL	CFW12101 CPR24259 CPR24260 CQB51070 CRZ40211
GB	AAF96816 ABQ19183 ACP07838 ACP11775 ACQ62378
REF	NP_233304 WP_000070924 WP_000070925 WP_000070926 WP_000070927