BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15079

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

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

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

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

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

Data sets:
Data typeCount
13C chemical shifts188
15N chemical shifts50
1H chemical shifts314

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ER382A1

Entities:

Entity 1, ER382A 61 residues - 7052.778 Da.

1   METSERSERASPTYRVALMETALATHRLYS
2   ASPGLYARGMETILELEUTHRASPGLYLYS
3   PROGLUILEASPASPASPTHRGLYLEUVAL
4   SERTYRHISASPGLNGLNGLYASNALAMET
5   GLNILEASNARGASPASPVALSERGLNILE
6   ILEGLUARGLEUGLUHISHISHISHISHIS
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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_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

Related Database Links:

PDB
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