BMRB Entry 16365

Name: Solution NMR structure of yeast protein YOR252W [residues 38-178]: Northeast Structural Genomics Consortium target YT654
Published: 2012-08-03

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PDB ID: 2kkm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16365
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of yeast protein YOR252W [residues 38-178]: Northeast Structural Genomics Consortium target YT654

Deposition date:

2009-06-26

Original release date:

2012-08-03

Authors:

Cort, John; Yee, Adelinda; Liu, Chengsong; Arrowsmith, Cheryl; Kennedy, Michael

Citation:

Citation: Cort, John; Yee, Adelinda; Liu, Chengsong; Arrowsmith, Cheryl; Kennedy, Michael. "Solution NMR structure of yeast protein YOR252W" .

Assembly members:

Assembly members:
YOR252W, polymer, 141 residues, Formula weight is not available

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YOR252W: MREDKIAAKKKLHQDKRVHE LARVKFMQDVVNSDTFKGQP IFDHAHTREFIQSFIERDDT ELDELKKKRRSNRPPSNRQV LLQQRRDQELKEFKAGFLCP DLSDAKNMEFLRNWNGTFGL LNTLRLIRINDKGEQVVGGN E

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	514
15N chemical shifts	133
1H chemical shifts	775

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YOR252W	1

Entities:

Entity 1, YOR252W 141 residues - Formula weight is not available

An N-term His purification tag was cleaved.

1

MET

ARG

GLU

ASP

LYS

ILE

ALA

LYS

2

LYS

LEU

HIS

GLN

ASP

LYS

ARG

VAL

HIS

GLU

3

LEU

ALA

ARG

VAL

LYS

PHE

MET

GLN

ASP

VAL

4

VAL

ASN

SER

ASP

THR

PHE

LYS

GLY

GLN

PRO

5

ILE

PHE

ASP

HIS

ALA

HIS

THR

ARG

GLU

PHE

6

ILE

GLN

SER

PHE

ILE

GLU

ARG

ASP

THR

7

GLU

LEU

ASP

GLU

LEU

LYS

ARG

8

SER

ASN

ARG

PRO

SER

ASN

ARG

GLN

VAL

9

LEU

GLN

ARG

ASP

GLN

GLU

LEU

10

LYS

GLU

PHE

LYS

ALA

GLY

PHE

LEU

CYS

PRO

11

ASP

LEU

SER

ASP

ALA

LYS

ASN

MET

GLU

PHE

12

LEU

ARG

ASN

TRP

ASN

GLY

THR

PHE

GLY

LEU

13

LEU

ASN

THR

LEU

ARG

LEU

ILE

ARG

ILE

ASN

14

ASP

LYS

GLY

GLU

GLN

VAL

GLY

ASN

15

GLU

Samples:

sample_1: YOR252W, [U-99% 13C; U-99% 15N], 0.6 mM; sodium chloride 300 mM; DTT 10 mM; benzamidine 1 mM; sodium azide 0.01%; H2O 93%; D2O 7%

sample_2: YOR252W, [U-99% 13C; U-99% 15N], 0.6 mM; sodium chloride 300 mM; DTT 10 mM; benzamidine 1 mM; sodium azide 0.01%; D2O 100%

sample_conditions_1: ionic strength: 300 mM; pH: 7; pressure: 1 atm; temperature: 293 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 CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
4D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1

Software:

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

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

PSVS, Bhattacharya and Montelione - refinement

SPARKY, Goddard - chemical shift assignment, peak picking

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Varian INOVA 750 MHz
Varian INOVA 800 MHz
Varian INOVA 600 MHz

PDB	2KKM
DBJ	GAA26563
EMBL	CAA99474 CAY86533
GB	AHY77532 AJP41762 AJT71184 AJT71672 AJT72162
REF	NP_014895
SP	Q08687
TPG	DAA11019
AlphaFold	Q08687