BMRB Entry 15288

Name: NMR solution structure of Bacillus subtilis YobA 21-120: Northeast Structural Genomics Consortium target SR547
Published: 2008-02-20

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PDB ID: 2jqo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15288
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of Bacillus subtilis YobA 21-120: Northeast Structural Genomics Consortium target SR547

Deposition date:

2007-06-06

Original release date:

2008-02-20

Authors:

Cort, John; Ramelot, Theresa; Cort, Chen; Jang, Mei; Cunningham, Kellie; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Cort, John. "NMR solution structure of Bacillus subtilis YobA 21-120" .

Assembly members:

Assembly members:
YobA 21-120, polymer, 108 residues, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: 1423 Superkingdom: Bacteria Kingdom: not available Genus/species: Bacillus subtilis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YobA 21-120: MNKNEQNGDETKMQSLVGYV VLKDNERAILITDTKAPGKE DYNLSEGQLMNKFKNNIVIV GLSEIDNTDDLKRGEKIKVW FHTRKESNPPSATIQKYELL LEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	456
15N chemical shifts	117
1H chemical shifts	751

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YobA 21-120	1

Entities:

Entity 1, YobA 21-120 108 residues - Formula weight is not available

Residue 2 in this entry corresponds to residue 21 in the public database sequence; the first 20 are a putative signal peptide sequence and have been truncated.

1

MET

ASN

LYS

ASN

GLU

GLN

ASN

GLY

ASP

GLU

2

THR

LYS

MET

GLN

SER

LEU

VAL

GLY

TYR

VAL

3

VAL

LEU

LYS

ASP

ASN

GLU

ARG

ALA

ILE

LEU

4

ILE

THR

ASP

THR

LYS

ALA

PRO

GLY

LYS

GLU

5

ASP

TYR

ASN

LEU

SER

GLU

GLY

GLN

LEU

MET

6

ASN

LYS

PHE

LYS

ASN

ILE

VAL

ILE

VAL

7

GLY

LEU

SER

GLU

ILE

ASP

ASN

THR

ASP

8

LEU

LYS

ARG

GLY

GLU

LYS

ILE

LYS

VAL

TRP

9

PHE

HIS

THR

ARG

LYS

GLU

SER

ASN

PRO

10

SER

ALA

THR

ILE

GLN

LYS

TYR

GLU

LEU

11

LEU

GLU

HIS

Samples:

NC: entity, [U-100% 13C; U-100% 15N], 0.75 mM; dithiothreitol 10 mM; calcium chloride 5 mM; sodium chloride 100 mM; ammonium acetate 20 mM; sodium azide 0.02%; H2O 95%; D2O 5%

NC5: entity, [5% 13C; U-100% N15], 0.79 mM; dithiothreitol 10 mM; calcium chloride 5 mM; sodium chloride 100 mM; ammonium acetate 20 mM; sodium azide 0.02%; H2O 95%; D2O 5%

NC_D2O: entity, [U-100% 13C; U-100% 15N], 0.75 mM; dithiothreitol 10 mM; calcium chloride 5 mM; sodium chloride 100 mM; ammonium acetate 20 mM; sodium azide 0.02%; D2O 100%

sample_conditions_1: pH: 4.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC5	isotropic	sample_conditions_1
3D CBCA(CO)NH	NC	isotropic	sample_conditions_1
3D HNCACB	NC	isotropic	sample_conditions_1
3D HBHA(CO)NH	NC	isotropic	sample_conditions_1
3D HCCH-TOCSY	NC	isotropic	sample_conditions_1
3D HNHA	NC	isotropic	sample_conditions_1
3D HNCO	NC	isotropic	sample_conditions_1
3D CCH-TOCSY	NC	isotropic	sample_conditions_1
3D 1H-15N NOESY	NC	isotropic	sample_conditions_1
3D 1H-13C NOESY	NC	isotropic	sample_conditions_1
4D 1H-13C-13C-1H HMQC-NOESY	NC_D2O	isotropic	sample_conditions_1

Software:

AutoStruct, Huang, Tejero, Powers and Montelione - structure solution

SPARKY, Goddard - data analysis

FELIX, Accelrys Software Inc. - processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

PSVS, Bhattacharya and Montelione - structure evaluation

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz

PDB	2JQO 4QY7
DBJ	BAM52538 BAM58113
EMBL	CAB13773 CEI57077 CEJ77502
GB	ADV92789 AFQ57816 AGG61259 AHA77924 AIC40308
REF	NP_389762 WP_003231383 WP_015714070 WP_029318065 WP_038429094
SP	O31835
AlphaFold	O31835