BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 15338

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

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

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

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

Data typeCount
13C chemical shifts330
15N chemical shifts74
1H chemical shifts508

Time Domain Data

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1protein1
2Zinc ion, 12
3Zinc ion, 22

Entities:

Entity 1, protein 81 residues - 9164.535 Da.

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

1   METGLUILETHRCYSPROVALCYSHISHIS
2   ALALEUGLUARGASNGLYASPTHRALAHIS
3   CYSGLUTHRCYSALALYSASPPHESERLEU
4   GLNALALEUCYSPROASPCYSARGGLNPRO
5   LEUGLNVALLEULYSALACYSGLYALAVAL
6   ASPTYRPHECYSGLNASNGLYHISGLYLEU
7   ILESERLYSLYSARGVALASNPHEVALILE
8   SERASPGLNLEUGLUHISHISHISHISHIS
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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC (aliph)sample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D aromatic 1H-13C NOESYsample_2isotropicsample_conditions_1
4D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQC (arom)sample_1isotropicsample_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

Related Database Links:

PDB
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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts