BMRB Entry 18086

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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/BMR18086
MolProbity Validation Chart

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Title:
GhoS (YjdK) monomer
Deposition date:
2011-11-16
Original release date:
2012-09-04
Authors:
Lord, Dana; Peti, Wolfgang; Page, Rebecca
Citation:

Citation: Wang, X.; Lord, D.; Cheng, H.; Osbourne, D.; Hong, S.; Sanchez-Torres, V.; Quiroga, C.; Zheng, K.; Herrmann, T.; Peti, W.; Benedik, M.; Page, R.; Wood, T.. "A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS"  Nat. Chem. Biol. ., .-. (2012).
PubMed: 22941047

Assembly members:

Assembly members:
YjdK, polymer, 100 residues, Formula weight is not available

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   Host organism: Escherichia coli   Vector: RP1B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YjdK: GHMEGKNKFNTYVVSFDYPS SYSSVFLRLRSLMYDMNFSS IVADEYGIPRQLNENSFAIT TSLAASEIEDLIRLKCLDLP DIDFDLNIMTVDDYFRQFYK

Data sets:
Data typeCount
13C chemical shifts304
15N chemical shifts103
1H chemical shifts712

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1YjdK1

Entities:

Entity 1, YjdK 100 residues - Formula weight is not available

G(1) and H(2) are cloning artifacts.

1   GLYHISMETGLUGLYLYSASNLYSPHEASN
2   THRTYRVALVALSERPHEASPTYRPROSER
3   SERTYRSERSERVALPHELEUARGLEUARG
4   SERLEUMETTYRASPMETASNPHESERSER
5   ILEVALALAASPGLUTYRGLYILEPROARG
6   GLNLEUASNGLUASNSERPHEALAILETHR
7   THRSERLEUALAALASERGLUILEGLUASP
8   LEUILEARGLEULYSCYSLEUASPLEUPRO
9   ASPILEASPPHEASPLEUASNILEMETTHR
10   VALASPASPTYRPHEARGGLNPHETYRLYS

Samples:

13C_15N-yjdK: YjdK, [U-99% 13C; U-99% 15N], 1.14 mM; sodium phosphate 20 mM; sodium chloride 100 mM; TCEP 0.5 mM; H2O 90%; D2O 10%

yjdk_sample: YjdK 1.76 mM; sodium phosphate 20 mM; sodium chloride 100 mM; TCEP 0.5 mM; D2O 100%

15N-yjdK: YjdK, [U-99% 15N], 1.42 mM; sodium phosphate 20 mM; sodium chloride 100 mM; TCEP 0.5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15N-yjdKisotropicsample_conditions_1
2D 1H-13C HSQC13C_15N-yjdKisotropicsample_conditions_1
3D HNCA13C_15N-yjdKisotropicsample_conditions_1
3D HNCACB13C_15N-yjdKisotropicsample_conditions_1
3D CBCA(CO)NH13C_15N-yjdKisotropicsample_conditions_1
3D C(CO)NH13C_15N-yjdKisotropicsample_conditions_1
3D HBHA(CO)NH13C_15N-yjdKisotropicsample_conditions_1
3D HCCH-TOCSY13C_15N-yjdKisotropicsample_conditions_1
3D 1H-15N NOESY15N-yjdKisotropicsample_conditions_1
3D 1H-13C NOESY13C_15N-yjdKisotropicsample_conditions_1
2D 1H-1H TOCSYyjdk_sampleisotropicsample_conditions_1
2D 1H-1H NOESYyjdk_sampleisotropicsample_conditions_1
2D 1H-1H COSYyjdk_sampleisotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ BAB38533 BAE78130 BAG79950 BAI28383 BAI33567
EMBL CAP78600 CAQ34477 CAR01103 CAR05785 CAR10820
GB AAA97028 AAC77089 AAG59327 AAZ90798 ABE10131
REF NP_313137 NP_418552 WP_000272165 WP_000272166 WP_000272167
SP P0AF61 P0AF62
AlphaFold P0AF61 P0AF62

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