BMRB Entry 15079

Name: Solution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A.
Published: 2007-02-23

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PDB ID: 2jn0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15079
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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:

Solution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A.

Deposition date:

2006-12-15

Original release date:

2007-02-23

Authors:

Rossi, Paolo; Chen, Chen; Jiang, Mei; Cunningham, Kellie; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano

Citation:

Citation: Rossi, Paolo; Chen, Chen; Jiang, Mei; Cunningham, Kellie; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano. "Solution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A." .

Assembly members:

Assembly members:
ER382A, polymer, 61 residues, 7052.778 Da.

Natural source:

Natural source: Common Name: E. 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: ER382A-21.2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ER382A: MSSDYVMATKDGRMILTDGK PEIDDDTGLVSYHDQQGNAM QINRDDVSQIIERLEHHHHH H

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	188
15N chemical shifts	50
1H chemical shifts	314

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ER382A	1

Entities:

Entity 1, ER382A 61 residues - 7052.778 Da.

1

MET

SER

ASP

TYR

VAL

MET

ALA

THR

LYS

2

ASP

GLY

ARG

MET

ILE

LEU

THR

ASP

GLY

LYS

3

PRO

GLU

ILE

ASP

THR

GLY

LEU

VAL

4

SER

TYR

HIS

ASP

GLN

GLY

ASN

ALA

MET

5

GLN

ILE

ASN

ARG

ASP

VAL

SER

GLN

ILE

6

ILE

GLU

ARG

LEU

GLU

HIS

7

HIS

Samples:

sample_1: ER382A, [U-100% 13C; U-100% 15N], 1.17 mM; DTT 10 mM; CaCl2 5 mM; NaCl 0.1 M; MES 20 mM; sodium azide 0.02%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; 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 HNCO	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 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

AutoStruct v2.1.1, Huang, Y-J.; Tejero, R.; Powers, R.; Montelione, G.T. - structure solution

NMRPipe v2005, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - structure anaylsis

SPARKY v3.110, Goddard, Kneller - data analysis

Molmol v2K.2, Koradi, Billeter and Wuthrich - structure visualization

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

Procheck v3.51, Laskowski and MacArthur - structure validation

X-PLOR NIH v2.11.2, Schwieters, Kuszewski, Tjandra and Clore - structure solution

DYANA v1.2, Guntert, Braun and Wuthrich - structure solution

MolProbity v3.01, Richardson - structure validation

QUEEN v1.1, Nabuurs, Spronk, Vriend, Vuister - structure refinement

xwinnmr v3.5, Bruker biospin - data collection

PSVS v1.2, Bhattacharya, Montelione - structure validation

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2JN0
DBJ	BAB37113 BAE76902 BAG78614 BAI27097 BAI32140
EMBL	CAP77290 CAQ33159 CAQ90261 CAQ99759 CAR04368
GB	AAB40480 AAC75872 AAG57945 AAN44329 AAN81873
REF	NP_311717 NP_417310 NP_708622 WP_000758652 WP_000758653
SP	P65294 P65295 P65296 P65297
AlphaFold	P65294 P65295 P65296 P65297