BMRB Entry 15338

Name: NMR Structure of Protein YfgJ from Salmonella Typhimurium. Northeast Structural Genomics Target StR86.
Published: 2007-08-02

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PDB ID: 2jrp
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/BMR15338
MolProbity Validation Chart

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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 YfgJ from Salmonella Typhimurium. Northeast Structural Genomics Target StR86.

Deposition date:

2007-06-28

Original release date:

2007-08-02

Authors:

Ding, Keyang; Ramelot, Theresa; Cort, John; Wang, Huang; Nwosu, Chioma; Cunningham, Kellie; Owens, Leah; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, Gurla; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Ding, Keyang; Ramelot, Theresa; Cort, John; Wang, Huang; Nwosu, Chioma; Cunningham, Kellie; Owens, Leah; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, Gurla; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael. "NMR Structure of Protein YfgJ from Salmonella Typhimurium." .

Assembly members:

Assembly members:
protein, polymer, 81 residues, 9164.535 Da.
ZN, non-polymer, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: 602 Superkingdom: Bacteria Kingdom: not available Genus/species: Salmonella typhimurium

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
protein: MEITCPVCHHALERNGDTAH CETCAKDFSLQALCPDCRQP LQVLKACGAVDYFCQNGHGL ISKKRVNFVISDQLEHHHHH H

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	330
15N chemical shifts	74
1H chemical shifts	508

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	protein	1
2	Zinc ion, 1	2
3	Zinc ion, 2	2

Entities:

Entity 1, protein 81 residues - 9164.535 Da.

The full sequence is cloned with his-tag LEHHHHHH added at the C terminal.

1

MET

GLU

ILE

THR

CYS

PRO

VAL

CYS

HIS

2

ALA

LEU

GLU

ARG

ASN

GLY

ASP

THR

ALA

HIS

3

CYS

GLU

THR

CYS

ALA

LYS

ASP

PHE

SER

LEU

4

GLN

ALA

LEU

CYS

PRO

ASP

CYS

ARG

GLN

PRO

5

LEU

GLN

VAL

LEU

LYS

ALA

CYS

GLY

ALA

VAL

6

ASP

TYR

PHE

CYS

GLN

ASN

GLY

HIS

GLY

LEU

7

ILE

SER

LYS

ARG

VAL

ASN

PHE

VAL

ILE

8

SER

ASP

GLN

LEU

GLU

HIS

9

HIS

Entity 2, Zinc ion, 1 - Formula weight is not available

1

ZN

Samples:

sample_1: protein, [U-100% 13C; U-100% 15N], 1 ± 0.2 mM; NH4OAc 20 ± 1 mM; NaCl 100 ± 5 mM; DTT 10 ± 1 mM; CaCl2 5 ± 1 mM; NaN3 0.02 ± 0.001 %; H2O 95%; D2O 5%

sample_2: protein, [U-100% 13C; U-100% 15N], 1 ± 0.2 mM; NH4OAc 20 ± 1 mM; NaCl 100 ± 5 mM; DTT 10 ± 1 mM; CaCl2 5 ± 1 mM; NaN3 0.02 ± 0.001 %; D2O 100%

sample_3: protein, [U-5% 13C; U-100% 15N], 1.7 ± 0.2 mM; NH4OAc 20 ± 1 mM; NaCl 100 ± 5 mM; DTT 10 ± 1 mM; CaCl2 5 ± 1 mM; NaN3 0.02 ± 0.001 %; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 100 M; pH: 4.5; 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 (aliph)	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	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 HNHA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D C(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 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D aromatic 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
4D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC (arom)	sample_1	isotropic	sample_conditions_1

Software:

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

X-PLOR NIH v2.15.0, Schwieters, Kuszewski, Tjandra and Clore - structure solution

AutoStruct v2.1.1, Huang, Tejero, Powers and Montelione - data analysis

SPARKY v3.1, Goddard - peak picking

NMRPipe vlinux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz

PDB	2JRP
DBJ	BAJ37479 BAP08460
EMBL	CAD02721 CAR34081 CAR38373 CAR58447 CBG25542
GB	AAL21412 AAO68061 AAP83330 AAV76366 AAX66421
PIR	AE0821
REF	NP_457050 NP_461453 WP_000402503 WP_000406465 WP_000406466