BMRB Entry 15217

Name: NMR SOLUTION STRUCTURE OF YKVR PROTEIN FROM BACILLUS SUBTILIS: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR358
Published: 2007-05-02

Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15217

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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 YKVR PROTEIN FROM BACILLUS SUBTILIS: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR358

Deposition date:

2007-04-18

Original release date:

2007-05-02

Authors:

Swapna, G.; Chi Ho, K.; Cunningham, K.; Ma, L.; Xiao, R.; Baran, M.; Acton, T.; Liu, J.; Rost, B.; Montelione, G.

Citation:

Citation: Swapna, G.; Chi Ho, K.; Cunningham, K.; Ma, L.; Xiao, R.; Baran, M.; Acton, T.; Liu, J.; Rost, B.; Montelione, G.. "NMR Solution Structure of Ykvr Protein from Bacillus Subtilis: Northeast Structural Genomics Consortium Target SR358" .

Assembly members:

Assembly members:
YKVR_PROTEIN, polymer, 105 residues, 12246.754 Da.

Natural source:

Natural source: Common Name: Bacteria Taxonomy ID: 1423 Superkingdom: not available 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):
YKVR_PROTEIN: MVKTLRLNNVTLEMAAYQEE SEPKRKIAFTLNVTSETYHD IAVLLYEKTFNVEVPERDLA FRGEMTNYSTSLTNLYEPGA VSEFYIEITEIDKNADSLEH HHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	353
15N chemical shifts	101
1H chemical shifts	716

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	full length protein	1

Entities:

Entity 1, full length protein 105 residues - 12246.754 Da.

1

MET

VAL

LYS

THR

LEU

ARG

LEU

ASN

VAL

2

THR

LEU

GLU

MET

ALA

TYR

GLN

GLU

3

SER

GLU

PRO

LYS

ARG

LYS

ILE

ALA

PHE

THR

4

LEU

ASN

VAL

THR

SER

GLU

THR

TYR

HIS

ASP

5

ILE

ALA

VAL

LEU

TYR

GLU

LYS

THR

PHE

6

ASN

VAL

GLU

VAL

PRO

GLU

ARG

ASP

LEU

ALA

7

PHE

ARG

GLY

GLU

MET

THR

ASN

TYR

SER

THR

8

SER

LEU

THR

ASN

LEU

TYR

GLU

PRO

GLY

ALA

9

VAL

SER

GLU

PHE

TYR

ILE

GLU

ILE

THR

GLU

10

ILE

ASP

LYS

ASN

ALA

ASP

SER

LEU

GLU

HIS

11

HIS

Samples:

sample_1: YKVR PROTEIN, [U-10% 13C; U-100% 15N], 1.17 mM; SODIUM AZIDE 0.02 mM; MES 20 mM; DTT 100 mM; NaCl 100 mM; CaCl2 5 mM

sample_2: YKVR PROTEIN, [U-100% 13C; U-100% 15N], 1.17 ± 0.2 mM; SODIUM AZIDE 0.02 mM; MES 20 mM; DTT 100 mM; NaCl 100 mM; CaCl2 5 mM

sample_3: YKVR PROTEIN, [U-100% 13C; U-100% 15N], 1.17 ± 0.2 mM; SODIUM AZIDE 0.02 mM; MES 20 mM; DTT 100 mM; NaCl 100 mM; CaCl2 5 mM

sample_conditions_1: ionic strength: 105 mM; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HBHANH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY (aliph)	sample_3	isotropic	sample_conditions_1
3D HcccoNH-TOCSY	sample_2	isotropic	sample_conditions_1
3D CccoNH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY (arom)	sample_3	isotropic	sample_conditions_1

Software:

CNS_1.1,_X-PLOR v2.0.6, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

AutoAssign v2.1, Zimmerman, Moseley, Kulikowski, Montelione - chemical shift assignment

AVS, Moseley and Montelione - validation of assignments

AutoStruct v2.1.1, Huang,Y-J.,Powers,R.,Montelione, G.T., Huang,Y-J, Tejero,R.,Powers,R.,Montelione, G.T. - structure solution

NMR spectrometers:

VARIAN INOVA 600 MHz
BRUKER AVANCE 600 MHz

PDB	2JN9
DBJ	BAI84986 BAM52020 BAM57597
EMBL	CAB13253 CCU57937 CEI56537 CEJ76960 CJS27153
GB	ADV96396 AFQ57311 AGA22143 AGE63229 AGG60748
REF	NP_389263 WP_003245399 WP_015252208 WP_017695059 WP_024572583
SP	O31683
AlphaFold	O31683