BMRB Entry 15839

Name: Solution structure of protein yiiF from Shigella flexneri serotype 5b (strain 8401) . Northeast Structural Genomics Consortium target sft1
Published: 2008-08-19

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PDB ID: 2k5j
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15839
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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 yiiF from Shigella flexneri serotype 5b (strain 8401) . Northeast Structural Genomics Consortium target sft1

Deposition date:

2008-06-28

Original release date:

2008-08-19

Authors:

Wu, Yibing; Singarapu, Kiran Kumar; Semesi, Anthony; Yee, Adelinda; Bansal, Sonal; Prestegard, James; Arrowsmith, Cheryl; Szyperski, Thomas

Citation:

Citation: Wu, Yibing; Singarapu, Kiran Kumar; Semesi, Anthony; Yee, Adelinda; Bansal, Sonal; Prestegard, James; Arrowsmith, Cheryl; Szyperski, Thomas. "Solution structure of protein yiiF from Shigella flexneri serotype 5b (strain 8401) . Northeast Structural Genomics Consortium target sft1" .

Assembly members:

Assembly members:
yiiF, polymer, 160 residues, 18488.877 Da.

Natural source:

Natural source: Common Name: Escherichia coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: BL21 DE3 gold magic

Entity Sequences (FASTA):

Entity Sequences (FASTA):
yiiF: MNSLAGIDMGRILLDLSNEV IKQLDDLEVQRNLPRADLLR EAVDQYLINQSQTARTSVPG IWQGCEEDGVEYQRKLREEW MNSLAGIDMGRILLDLSNEV IKQLDDLEVQRNLPRADLLR EAVDQYLINQSQTARTSVPG IWQGCEEDGVEYQRKLREEW

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	261
15N chemical shifts	84
1H chemical shifts	559

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	yiiF	1

Entities:

Entity 1, yiiF 160 residues - 18488.877 Da.

1	MET	ASN	SER	LEU	ALA	GLY	ILE	ASP	MET	GLY
2	ARG	ILE	LEU	LEU	ASP	LEU	SER	ASN	GLU	VAL
3	ILE	LYS	GLN	LEU	ASP	ASP	LEU	GLU	VAL	GLN
4	ARG	ASN	LEU	PRO	ARG	ALA	ASP	LEU	LEU	ARG
5	GLU	ALA	VAL	ASP	GLN	TYR	LEU	ILE	ASN	GLN
6	SER	GLN	THR	ALA	ARG	THR	SER	VAL	PRO	GLY
7	ILE	TRP	GLN	GLY	CYS	GLU	GLU	ASP	GLY	VAL
8	GLU	TYR	GLN	ARG	LYS	LEU	ARG	GLU	GLU	TRP
9	MET	ASN	SER	LEU	ALA	GLY	ILE	ASP	MET	GLY
10	ARG	ILE	LEU	LEU	ASP	LEU	SER	ASN	GLU	VAL
11	ILE	LYS	GLN	LEU	ASP	ASP	LEU	GLU	VAL	GLN
12	ARG	ASN	LEU	PRO	ARG	ALA	ASP	LEU	LEU	ARG
13	GLU	ALA	VAL	ASP	GLN	TYR	LEU	ILE	ASN	GLN
14	SER	GLN	THR	ALA	ARG	THR	SER	VAL	PRO	GLY
15	ILE	TRP	GLN	GLY	CYS	GLU	GLU	ASP	GLY	VAL
16	GLU	TYR	GLN	ARG	LYS	LEU	ARG	GLU	GLU	TRP

Samples:

sample_1: entity, [U-100% 13C; U-100% 15N], 0.8 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_2: entity, [U-10% 13C; U-100% 15N], 0.8 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 0.3 M; pH: 7.0; 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_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
4,3D, GFT HNNCABCA	sample_1	isotropic	sample_conditions_1
4,3D, GFT CABCACONNH	sample_1	isotropic	sample_conditions_1
4,3D, GFT HCCH COSY	sample_1	isotropic	sample_conditions_1
4,3D, GFT HAHB(CABCACO)NNH	sample_1	isotropic	sample_conditions_1
3D, 15N-13C RESOLVEDSIMULTANIOUS NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1

Software:

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

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

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

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

XEASY, Bartels et al. - peak picking

NMR spectrometers:

Varian INOVA 750 MHz

PDB	2K5J
DBJ	BAG79700 BAJ45617
EMBL	CCJ46517 CCK49196 CDP72801 CDP77332 CDU39992
GB	AAB03023 AAN45401 AAP18799 AAZ90576 ABB68355
REF	NP_709694 WP_001086388 WP_001086390 WP_001087409 WP_001612096

1	MET	ASN	SER	LEU	ALA	GLY	ILE	ASP	MET	GLY
2	ARG	ILE	LEU	LEU	ASP	LEU	SER	ASN	GLU	VAL
3	ILE	LYS	GLN	LEU	ASP	ASP	LEU	GLU	VAL	GLN
4	ARG	ASN	LEU	PRO	ARG	ALA	ASP	LEU	LEU	ARG
5	GLU	ALA	VAL	ASP	GLN	TYR	LEU	ILE	ASN	GLN
6	SER	GLN	THR	ALA	ARG	THR	SER	VAL	PRO	GLY
7	ILE	TRP	GLN	GLY	CYS	GLU	GLU	ASP	GLY	VAL
8	GLU	TYR	GLN	ARG	LYS	LEU	ARG	GLU	GLU	TRP
9	MET	ASN	SER	LEU	ALA	GLY	ILE	ASP	MET	GLY
10	ARG	ILE	LEU	LEU	ASP	LEU	SER	ASN	GLU	VAL
11	ILE	LYS	GLN	LEU	ASP	ASP	LEU	GLU	VAL	GLN
12	ARG	ASN	LEU	PRO	ARG	ALA	ASP	LEU	LEU	ARG
13	GLU	ALA	VAL	ASP	GLN	TYR	LEU	ILE	ASN	GLN
14	SER	GLN	THR	ALA	ARG	THR	SER	VAL	PRO	GLY
15	ILE	TRP	GLN	GLY	CYS	GLU	GLU	ASP	GLY	VAL
16	GLU	TYR	GLN	ARG	LYS	LEU	ARG	GLU	GLU	TRP

1	MET	ASN	SER	LEU	ALA	GLY	ILE	ASP	MET	GLY
2	ARG	ILE	LEU	LEU	ASP	LEU	SER	ASN	GLU	VAL
3	ILE	LYS	GLN	LEU	ASP	ASP	LEU	GLU	VAL	GLN
4	ARG	ASN	LEU	PRO	ARG	ALA	ASP	LEU	LEU	ARG
5	GLU	ALA	VAL	ASP	GLN	TYR	LEU	ILE	ASN	GLN
6	SER	GLN	THR	ALA	ARG	THR	SER	VAL	PRO	GLY
7	ILE	TRP	GLN	GLY	CYS	GLU	GLU	ASP	GLY	VAL
8	GLU	TYR	GLN	ARG	LYS	LEU	ARG	GLU	GLU	TRP
9	MET	ASN	SER	LEU	ALA	GLY	ILE	ASP	MET	GLY
10	ARG	ILE	LEU	LEU	ASP	LEU	SER	ASN	GLU	VAL
11	ILE	LYS	GLN	LEU	ASP	ASP	LEU	GLU	VAL	GLN
12	ARG	ASN	LEU	PRO	ARG	ALA	ASP	LEU	LEU	ARG
13	GLU	ALA	VAL	ASP	GLN	TYR	LEU	ILE	ASN	GLN
14	SER	GLN	THR	ALA	ARG	THR	SER	VAL	PRO	GLY
15	ILE	TRP	GLN	GLY	CYS	GLU	GLU	ASP	GLY	VAL
16	GLU	TYR	GLN	ARG	LYS	LEU	ARG	GLU	GLU	TRP