BMRB Entry 6102

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR6102
MolProbity Validation Chart

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Title:
Solution structure of conserved protein YbeD from E. coli
Deposition date:
2004-02-19
Original release date:
2005-01-20
Authors:
Kozlov, G.; Gehring, K.
Citation:

Citation: Kozlov, G.; Elias, D.; Semesi, A.; Cygler, M.; Gehring, K.. "Structural similarity of Ybed protein from Escherichia coli to allosteric regulatory domains"  J. Bacteriol. 186, 8083-8088 (2004).

Assembly members:

Assembly members:
YbeD, polymer, 109 residues, 12403 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YbeD: MGTSHHHHHHSSGRENLYFQ GHMKTKLNELLEFPTPFTYK VMGQALPELVDQVVEVVQRH APGDYTPTVKPSSKGNYHSV SITINATHIEQVETLYEELG KIDIVRMVL

Data sets:
Data typeCount
1H chemical shifts434
13C chemical shifts157
15N chemical shifts78

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1YbeD, chain 11
2YbeD, chain 21

Entities:

Entity 1, YbeD, chain 1 109 residues - 12403 Da.

1   METGLYTHRSERHISHISHISHISHISHIS
2   SERSERGLYARGGLUASNLEUTYRPHEGLN
3   GLYHISMETLYSTHRLYSLEUASNGLULEU
4   LEUGLUPHEPROTHRPROPHETHRTYRLYS
5   VALMETGLYGLNALALEUPROGLULEUVAL
6   ASPGLNVALVALGLUVALVALGLNARGHIS
7   ALAPROGLYASPTYRTHRPROTHRVALLYS
8   PROSERSERLYSGLYASNTYRHISSERVAL
9   SERILETHRILEASNALATHRHISILEGLU
10   GLNVALGLUTHRLEUTYRGLUGLULEUGLY
11   LYSILEASPILEVALARGMETVALLEU

Samples:

sample_1: YbeD, [U-13C; U-15N], 2 mM; phosphate buffer 50 mM; NaCl 300 mM; sodium azide 0.1 mM; H2O 90%; D2O 10%

sample_2: YbeD, [U-15N], 2 mM; phosphate buffer 50 mM; NaCl 300 mM; sodium azide 0.1 mM; H2O 90%; D2O 10%

sample_3: YbeD 2 mM; phosphate buffer 50 mM; NaCl 300 mM; sodium azide 0.1 mM; D2O 100%

sample_cond_1: pH: 6.3; temperature: 298 K; ionic strength: 300 mM; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
3D 15N-separated NOESYnot availablenot availablesample_cond_1
HNHAnot availablenot availablesample_cond_1
2D NOESYnot availablenot availablesample_cond_1

Software:

XWINNMR v2.1 - collection, processing

GIFA v4.31 - processing

XEASY v1.3.13 - data analysis

CYANA v1.0.6 - structure solution

Xplor-NIH v2.9.2 - refinement

NMR spectrometers:

  • Bruker DRX 500 MHz

Related Database Links:

PDB
DBJ BAA35274 BAB34092 BAG76222 BAI24034 BAI29501
EMBL CAD05113 CAP75130 CAQ31106 CAQ89971 CAQ97484
GB AAA66341 AAB40831 AAC73732 AAG54965 AAL19587
PIR AG0580
REF NP_286357 NP_308696 NP_415164 NP_455212 NP_459628
SP A1A8Q6 A7ZJ19 A7ZXQ8 A8AJH3 A9MKE1
AlphaFold A1A8Q6 A7ZJ19 A7ZXQ8 A8AJH3 A9MKE1

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks