BMRB Entry 18283

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR18283
MolProbity Validation Chart

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Title:
Assignment of E coli periplasmic protein YmgD
Deposition date:
2012-02-20
Original release date:
2013-04-15
Authors:
Wu, Kuen-Phon; Inouye, Masayori; Baum, Jean
Citation:

Citation: Wu, Kuen-Phon; Masuda, Hisako; Hsu, Shang-Te; Baum, Jean; Inouye, Masayori. "Solution structure of homodimeric periplasmic protein YmgD in E. coli"  J. Biol. Chem. ., .-..

Assembly members:

Assembly members:
YmgD, polymer, 90 residues, Formula weight is not available

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: pET21c

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YmgD: QDYNIKNGLPSETYITCAEA NEMAKTDSAQVAEIVAVMGN ASVASRDLKIEQSPELSAKV VEKLNQVCAKDPQMLLITAI DDTMRAIGKK

Data sets:
Data typeCount
13C chemical shifts342
15N chemical shifts96
1H chemical shifts596

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

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

Entities:

Entity 1, YmgD, chain 1 90 residues - Formula weight is not available

1   GLNASPTYRASNILELYSASNGLYLEUPRO
2   SERGLUTHRTYRILETHRCYSALAGLUALA
3   ASNGLUMETALALYSTHRASPSERALAGLN
4   VALALAGLUILEVALALAVALMETGLYASN
5   ALASERVALALASERARGASPLEULYSILE
6   GLUGLNSERPROGLULEUSERALALYSVAL
7   VALGLULYSLEUASNGLNVALCYSALALYS
8   ASPPROGLNMETLEULEUILETHRALAILE
9   ASPASPTHRMETARGALAILEGLYLYSLYS

Samples:

CN-YmgD: YmgD, [U-99% 13C; U-99% 15N], 0.4 mM; H2O 90%; D2O 10%; Sodium acetate 100 mM; NaCl 50 mM

pH_5.0: ionic strength: 0.05 M; pH: 5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCCN-YmgDisotropicpH_5.0
2D 1H-13C HSQCCN-YmgDisotropicpH_5.0
2D 1H-13C HSQC aliphaticCN-YmgDisotropicpH_5.0
3D HNCOCN-YmgDisotropicpH_5.0
3D HN(CA)COCN-YmgDisotropicpH_5.0
3D C(CO)NHCN-YmgDisotropicpH_5.0
3D HNCACBCN-YmgDisotropicpH_5.0
3D H(CCO)NHCN-YmgDisotropicpH_5.0
3D HCCH-TOCSYCN-YmgDisotropicpH_5.0
3D CBCA(CO)NHCN-YmgDisotropicpH_5.0
3D 1H-15N NOESYCN-YmgDisotropicpH_5.0
3D 1H-15N TOCSYCN-YmgDisotropicpH_5.0
3D 1H-13C NOESYCN-YmgDisotropicpH_5.0

Software:

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

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

  • Varian INOVA 800 MHz

Related Database Links:

PDB
DBJ BAA36005 BAG76740 BAI24982 BAI30108 BAI35428
EMBL CAP75703 CAQ31672 CAQ98049 CAR02560 CAR07513
GB AAC74255 AAN42775 AAN80081 AAP16666 AAZ87885
REF NP_415689 NP_707068 WP_000219597 WP_000531016 WP_000712685
SP P0AB46 P0AB47 P0AB48
AlphaFold P0AB46 P0AB47 P0AB48

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