BMRB Entry 15762

Name: NMR Structure of Protein yiiS from Shigella flexneri: Northeast Structural Genomics Consortium Target SfR90
Published: 2008-05-09

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PDB ID: 2k3i
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15762
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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 Structure of Protein yiiS from Shigella flexneri: Northeast Structural Genomics Consortium Target SfR90

Deposition date:

2008-05-08

Original release date:

2008-05-09

Authors:

Mills, Jeffrey; Singarapu, Kiran Kumar; Eletski, Alex; Sukumaran, Dinesh; Wang, Dongyang; Jiang, Mei; Ciccosanti, Colleen; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Szyperski, Thomas

Citation:

Citation: Mills, Jeffrey; Singarapu, Kiran Kumar; Eletski, Alex; Sukumaran, Dinesh; Wang, Dongyang; Jiang, Mei; Ciccosanti, Colleen; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G. V. T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Szyperski, Thomas. "NMR STRUCTURE OF PROTEIN YIIS FROM SHIGELLA FLEXNERI: NORTHEAST STRUCTURAL GENOMICS TARGET SFR90" .

Assembly members:

Assembly members:
SfR90, polymer, 109 residues, 12030.683 Da.

Natural source:

Natural source: Common Name: Shigella flexneri Taxonomy ID: 623 Superkingdom: Bacteria Kingdom: not available Genus/species: Shigella flexneri

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SfR90: MAMKDVVDKCSTKGCAIDIG TVIDNDNCTSKFSRFFATRE EAESFMTKLKELAAAASSAD EGASVAYKIKDLEGQVELDA AFTFSCQAEMIIFELSLRSL ALEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	417
15N chemical shifts	105
1H chemical shifts	683

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SfR90	1

Entities:

Entity 1, SfR90 109 residues - 12030.683 Da.

1

MET

ALA

MET

LYS

ASP

VAL

ASP

LYS

CYS

2

SER

THR

LYS

GLY

CYS

ALA

ILE

ASP

ILE

GLY

3

THR

VAL

ILE

ASP

ASN

ASP

ASN

CYS

THR

SER

4

LYS

PHE

SER

ARG

PHE

ALA

THR

ARG

GLU

5

GLU

ALA

GLU

SER

PHE

MET

THR

LYS

LEU

LYS

6

GLU

LEU

ALA

SER

ALA

ASP

7

GLU

GLY

ALA

SER

VAL

ALA

TYR

LYS

ILE

LYS

8

ASP

LEU

GLU

GLY

GLN

VAL

GLU

LEU

ASP

ALA

9

ALA

PHE

THR

PHE

SER

CYS

GLN

ALA

GLU

MET

10

ILE

PHE

GLU

LEU

SER

LEU

ARG

SER

LEU

11

ALA

LEU

GLU

HIS

Samples:

sample_1: SfR90, [U-100% 13C; U-100% 15N], 1.1 mM; DSS 50 uM; NaN3 0.02%; DTT 100 mM; CaCl2 5 mM; NaCl 100 mM; MES 20 mM

sample_2: SfR90, [U-5% 13C; U-100% 15N], 1.02 mM; DSS 50 uM; NaN3 0.02%; DTT 100 mM; CaCl2 5 mM; NaCl 100 mM; MES 20 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 6.5; pressure: 1 atm; temperature: 298 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 HNCO	sample_1	isotropic	sample_conditions_1
4,3 D GFT HNNACBCA	sample_1	isotropic	sample_conditions_1
4,3 D GFT CABCACONHN	sample_1	isotropic	sample_conditions_1
4,3D HABCABCONHN	sample_1	isotropic	sample_conditions_1
4,3D GFT HCCH COSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D SimNOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1

Software:

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

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

XEASY, Bartels et al. - chemical shift assignment, data analysis

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

VNMRJ, Varian - collection

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

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

PSVS, Bhattacharya and Montelione - structure solution

TALOS, Cornilescu, Delaglio and Bax - structure solution

NMR spectrometers:

Varian INOVA 750 MHz

PDB	2K3I
DBJ	BAB38270 BAE77388 BAG79735 BAI27828 BAI33302
EMBL	CAP78379 CAQ34273 CAR00898 CAR05552 CAR10594
GB	AAB03054 AAC76904 AAG59115 AAN45433 AAN83302
REF	NP_312874 NP_418357 NP_709726 WP_000655983 WP_000655984
SP	P32162
AlphaFold	P32162