BMRB Entry 16065

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16065
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Structure of E. coli toxin RelE(R81A/R83A)mutant in complex with antitoxin RelBc (K47-L79) peptide
Deposition date:
2008-12-17
Original release date:
2009-04-22
Authors:
Li, Guang-Yao; Zhang, Yonglong; Inouye, Masayori; Ikura, Mitsuhiko
Citation:

Citation: Li, Guang-Yao; Zhang, Yonglong; Inouye, Masayori; Ikura, Mitsuhiko. "Inhibitory mechanism of E. coli RelE/RelB toxin/antitoxin module involves a helix displacement near a mRNA interferase active site"  J. Biol. Chem. 284, 14628-14636 (2009).
PubMed: 19297318

Assembly members:

Assembly members:
RelE, polymer, 98 residues, 11336.2 Da.
RelBc, polymer, 36 residues, 4128.7 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   Host organism: Escherichia coli   Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RelE: GSHMAYFLDFDERALKEWRK LGSTVREQLKKKLVEVLESP RIEANKLRGMPDCYKIKLRS SGYRLVYQVIDEKVVVFVIS VGKAEASEVYSEAVKRIL
RelBc: GSHKQTLLSDEDAELVEIVK ERLRNPKPVRVTLDEL

Data sets:
Data typeCount
13C chemical shifts496
15N chemical shifts127
1H chemical shifts993

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1subunit A1
2subunit B2

Entities:

Entity 1, subunit A 98 residues - 11336.2 Da.

Residues 1-3 represent a non-native cloning artifact from the affinity tag.

1   GLYSERHISMETALATYRPHELEUASPPHE
2   ASPGLUARGALALEULYSGLUTRPARGLYS
3   LEUGLYSERTHRVALARGGLUGLNLEULYS
4   LYSLYSLEUVALGLUVALLEUGLUSERPRO
5   ARGILEGLUALAASNLYSLEUARGGLYMET
6   PROASPCYSTYRLYSILELYSLEUARGSER
7   SERGLYTYRARGLEUVALTYRGLNVALILE
8   ASPGLULYSVALVALVALPHEVALILESER
9   VALGLYLYSALAGLUALASERGLUVALTYR
10   SERGLUALAVALLYSARGILELEU

Entity 2, subunit B 36 residues - 4128.7 Da.

Residues 1-3 represent a cloning artifact from the affinity tag.

1   GLYSERHISLYSGLNTHRLEULEUSERASP
2   GLUASPALAGLULEUVALGLUILEVALLYS
3   GLUARGLEUARGASNPROLYSPROVALARG
4   VALTHRLEUASPGLULEU

Samples:

sample_1: RelE, [U-13C; U-15N], 0.5 ± 0.2 mM; RelBc 0.5 ± 0.2 mM; sodium phosphate 25 ± 0 mM; sodium chloride 500 ± 0 mM; DTT 1 ± 0 mM; sodium azide 0.5 ± 0 mM

sample_2: RelE 0.5 ± 0.1 mM; RelBc, [U-13C; U-15N], 0.5 ± 0.1 mM; sodium phosphate 25 ± 2.5 mM; sodium chloride 500 ± 50 mM; DTT 1 ± 0.1 mM; sodium azide 0.5 ± 0.1 mM

sample_3: RelE, [U-13C; U-15N], 0.5 ± 0.1 mM; RelBc 0.5 ± 0.1 mM; sodium phosphate 25 ± 2.5 mM; sodium chloride 500 ± 50 mM; DTT 1 ± 0.1 mM; sodium azide 0.5 ± 0.1 mM

sample_4: RelE 0.5 ± 0.1 mM; RelBc, [U-13C; U-15N], 0.5 ± 0.1 mM; sodium phosphate 25 ± 2.5 mM; sodium chloride 500 ± 50 mM; DTT 1 ± 0.1 mM; sodium azide 0.5 ± 0.1 mM

sample_conditions_1: ionic strength: 0.5 M; pH: 6.5; pressure: 1 atm; temperature: 296.5 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HCCH-COSYsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
3D HCCH-COSYsample_4isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1
3D X-filtered 1H-13C NOESYsample_3isotropicsample_conditions_1
3D X-filtered 1H-13C NOESYsample_4isotropicsample_conditions_1

Software:

TOPSPIN v2.0, Bruker Biospin - collection

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

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - automated NOE peak assignments, structure calculation

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - Structure analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

VNMR, Varian - collection

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz
  • Varian INOVA 500 MHz

Related Database Links:

BMRB 16066 16067
PDB
DBJ BAA15262 BAI25452 BAJ43363 BAA15263 BAI25453 BAJ43364
EMBL CAA26251 CBG34537 CCF87938 CDJ71963 CDP71409 CAA26250 CAQ98463 CBG34538 CBK86917 CCF87937
GB AAC74636 AAN43137 AAP17028 AAS76442 ABQ02944 AAC74637 AAN43138 AAP17029 ABF03723 ABP62831
REF NP_416081 NP_707430 WP_000323024 WP_000323025 WP_001513653 NP_416082 NP_707431 NP_837222 WP_000534858 WP_001413280
SP P0C077 P0C078 P0C079 P0C080
AlphaFold P0C077 P0C078 P0C079 P0C080

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