BMRB Entry 19327

Name: Solution NMR Structure of yahO protein from Salmonella typhimurium, Northeast Structural Genomics Consortium (NESG) Target StR106
Published: 2013-08-26

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PDB ID: 2ma4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19327
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR Structure of yahO protein from Salmonella typhimurium, Northeast Structural Genomics Consortium (NESG) Target StR106

Deposition date:

2013-06-27

Original release date:

2013-08-26

Authors:

Eletsky, Alexander; Zhang, Qi; Liu, Gaohua; Wang, Huang; Nwosu, Chioma; Cunningham, Kellie; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Szyperski, Thomas

Citation:

Citation: Eletsky, Alexander; Zhang, Qi; Liu, Gaohua; Wang, Huang; Nwosu, Chioma; Cunningham, Kellie; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Szyperski, Thomas. "Solution NMR Structure of yahO protein from Salmonella typhimurium" To be published ., .-..

Assembly members:

Assembly members:
StR106, polymer, 78 residues, 8744.936 Da.

Natural source:

Natural source: Common Name: Salmonella typhimurium Taxonomy ID: 99287 Superkingdom: Bacteria Kingdom: not available Genus/species: Salmonella typhimurium

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21_NESG

Entity Sequences (FASTA):

Entity Sequences (FASTA):
StR106: AEIMKKTDFDKVASEYTKIG TISTTGEMSPLDAREDLIKK ADEKGADVVVLTSGQTENKI HGTADIYKKKLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	252
15N chemical shifts	75
1H chemical shifts	519

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	yahO protein	1

Entities:

Entity 1, yahO protein 78 residues - 8744.936 Da.

Residues 92-99 represent a non-native affinity purification tag

1

ALA

GLU

ILE

MET

LYS

THR

ASP

PHE

ASP

2

LYS

VAL

ALA

SER

GLU

TYR

THR

LYS

ILE

GLY

3

THR

ILE

SER

THR

GLY

GLU

MET

SER

PRO

4

LEU

ASP

ALA

ARG

GLU

ASP

LEU

ILE

LYS

5

ALA

ASP

GLU

LYS

GLY

ALA

ASP

VAL

6

LEU

THR

SER

GLY

GLN

THR

GLU

ASN

LYS

ILE

7

HIS

GLY

THR

ALA

ASP

ILE

TYR

LYS

8

LEU

GLU

HIS

Samples:

NC: StR106, [U-100% 13C; U-100% 15N], 1.1 mM; NaN3 0.02%; DTT 10 mM; calcium chloride 5 mM; sodium chloride 100 mM; ammonium acetate 20 mM; DSS 50 uM; H2O 90%; D2O 10%

NC5: StR106, [5% 13C; U-100% 15N], 1 mM; NaN3 0.02%; DTT 10 mM; calcium chloride 5 mM; sodium chloride 100 mM; ammonium acetate 20 mM; DSS 50 uM; H2O 90%; D2O 10%

NC_D2O: StR106, [U-100% 13C; U-100% 15N], 0.3 mM; NaN3 0.02%; DTT 10 mM; calcium chloride 5 mM; sodium chloride 100 mM; ammonium acetate 20 mM; DSS 50 uM; D2O 100%

sample_conditions_1: pH: 4.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	NC	isotropic	sample_conditions_1
3D HNCO	NC	isotropic	sample_conditions_1
(4,3)D GFT CABCA(CO)NHN	NC	isotropic	sample_conditions_1
(4,3)D GFT HNHNCABCA	NC	isotropic	sample_conditions_1
(4,3)D GFT HABCAB(CO)NHN	NC	isotropic	sample_conditions_1
3D 1H-15N,13C NOESY	NC	isotropic	sample_conditions_1
(4,3)D GFT HCCH-COSY aliphatic	NC	isotropic	sample_conditions_1
3D (H)CCH-COSY aromatic	NC	isotropic	sample_conditions_1
3D (H)CCH-TOCSY aliphatic	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	NC	isotropic	sample_conditions_1
2D 1H-13C HSQC methyl	NC5	isotropic	sample_conditions_1
2D 1H-15N HSQC	NC_D2O	isotropic	sample_conditions_1

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement, geometry optimization, structure solution

AS-DP v1.0, Huang, Tejero, Powers and Montelione - structure calculation, refinement

XEASY v1.3.13, Bartels et al., Keller and Wuthrich - data analysis, data analysis,peak picking,chemical shift assignment

VNMRJ v2.2D, Varian - collection

TALOS+, Shen, Cornilescu, Delaglio and Bax - geometry optimization

PSVS v1.4, Bhattacharya, Montelione - structure validation

XEASY v1.3.13, Bartels et al., Keller and Wuthrich - data analysis, data analysis,peak picking,chemical shift assignment

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PROSA v6.4, Guntert - processing

DYANA v1.5, Guntert, Braun and Wuthrich - data analysis

UBNMR v1.0, Shen - data analysis

NMR spectrometers:

Varian INOVA 750 MHz

UNP	Q7CR49
PDB	2MA4 2NOC
DBJ	BAJ35371 BAP06126
EMBL	CAC12674 CAD08821 CAR31935 CAR36277 CAR60410
GB	AAL19320 AAO70086 AAV78241 AAX64313 ABX68592
PIR	AE0547
REF	NP_454961 NP_459361 WP_000848022 WP_000848024 WP_000848025
AlphaFold	Q7CR49