BMRB Entry 16490

Name: Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929
Published: 2009-10-06

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PDB ID: 2ko6
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/BMR16490
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929

Deposition date:

2009-09-10

Original release date:

2009-10-06

Authors:

Wu, Bin; Yee, Adelinda; Fares, Christophe; Lemak, Alexander; Semest, Anthony; Arrowsmith, Cheryl

Citation:

Citation: Wu, Bin; Yee, Adelinda; Fares, Christophe; Lemak, Alexander; Semest, Anthony; Arrowsmith, Cheryl. "Solution Structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929" .

Assembly members:

Assembly members:
sf3929, polymer, 89 residues, 10322.015 Da.

Natural source:

Natural source: Common Name: shigella flexneri 2a Taxonomy ID: 42897 Superkingdom: Bacteria Kingdom: not available Genus/species: Shigella flexneri

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: p15Tvlic

Entity Sequences (FASTA):

Entity Sequences (FASTA):
sf3929: MKCKRLNEVIELLQPAWQKE PDFNLLQFLQKLAKESGFDG ELADLTDDILIYHLKMRDSA KDAVIPGLQKDYEEDFKTAL LRARGVIKE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	369
15N chemical shifts	88
1H chemical shifts	612

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	sf3929	1

Entities:

Entity 1, sf3929 89 residues - 10322.015 Da.

1

MET

LYS

CYS

LYS

ARG

LEU

ASN

GLU

VAL

ILE

2

GLU

LEU

GLN

PRO

ALA

TRP

GLN

LYS

GLU

3

PRO

ASP

PHE

ASN

LEU

GLN

PHE

LEU

GLN

4

LYS

LEU

ALA

LYS

GLU

SER

GLY

PHE

ASP

GLY

5

GLU

LEU

ALA

ASP

LEU

THR

ASP

ILE

LEU

6

ILE

TYR

HIS

LEU

LYS

MET

ARG

ASP

SER

ALA

7

LYS

ASP

ALA

VAL

ILE

PRO

GLY

LEU

GLN

LYS

8

ASP

TYR

GLU

ASP

PHE

LYS

THR

ALA

LEU

9

LEU

ARG

ALA

ARG

GLY

VAL

ILE

LYS

GLU

Samples:

sample_1: sf3929, [U-100% 13C; U-100% 15N], 0.5 mM; TRIS, [U-100% 2H], 10 mM; sodium chloride 300 mM; zinc sulphate 10 uM; DTT, [U-100% 2H], 10 mM; benzamidine 10 mM; inhibitor cocktail 1 x; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 300 mM; pH: 7; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D C(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 CCH-TOCSY	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
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

MDDGUI v1.0, Gutmanas and Arrowsmith - processing

SPARKY v3.95, Goddard - data analysis, peak picking

FAWN v1.0, Lemak and Arrowsmith - chemical shift assignment

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

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

AutoStruct, Huang, Tejero, Powers and Montelione - NMR structure quality assessment

PSVS, Bhattacharya and Montelione - NMR structure quality assessment

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

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

PDB	2KO6
DBJ	BAB38204 BAE77450 BAG79663 BAI27894 BAI33017
EMBL	CAP78316 CAQ34210 CAQ91090 CAR00828 CAR05492
GB	AAB02993 AAC76856 AAG59047 AAN45364 AAN83233
REF	NP_312808 NP_418295 NP_709657 WP_001295263 WP_001329922
SP	P0ADP9 P0ADQ0 P0ADQ1
AlphaFold	P0ADP9 P0ADQ0 P0ADQ1