BMRB Entry 34717

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34717
MolProbity Validation Chart

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Title:
Structure of the ADP-ribosyltransferase TccC3HVR from Photorhabdus Luminescens
Deposition date:
2022-03-24
Original release date:
2022-06-21
Authors:
Lindemann, F.; Belyy, A.; Friedrich, D.; Schmieder, P.; Bardiaux, B.; Roderer, D.; Funk, J.; Protze, J.; Bieling, P.; Oschkinat, H.; Raunser, S.
Citation:

Citation: Belyy, Alexander; Lindemann, Florian; Roderer, Daniel; Funk, Johanna; Bardiaux, Benjamin; Protze, Jonas; Bieling, Peter; Oschkinat, Hartmut; Raunser, Stefan. "Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin"  Nat. Commun. 13, 4202-4202 (2022).
PubMed: 35858890

Assembly members:

Assembly members:
entity_1, polymer, 194 residues, 21723.785 Da.

Natural source:

Natural source:   Common Name: Photorhabdus luminescens   Taxonomy ID: 29488   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Photorhabdus luminescens

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MSTTSTNLQKKSFTLYRADN RSFEEMQSKFPEGFKAWTPL DTKMARQFASIFIGQKDTSN LPKETVKNISTWGAKPKLKD LSNYIKYTKDKSTVWVSTAI NTEAGGQSSGAPLHKIDMDL YEFAIDGQKLNPLPEGRTKN MVPSLLLDTPQIETSSIIAL NHGPVNDAEISFLTTIPLKN VKPHKRGTLEVLFQ

Data typeCount
13C chemical shifts634
15N chemical shifts194
1H chemical shifts1239

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1TccC31

Entities:

Entity 1, TccC3 194 residues - 21723.785 Da.

1   METSERTHRTHRSERTHRASNLEUGLNLYS
2   LYSSERPHETHRLEUTYRARGALAASPASN
3   ARGSERPHEGLUGLUMETGLNSERLYSPHE
4   PROGLUGLYPHELYSALATRPTHRPROLEU
5   ASPTHRLYSMETALAARGGLNPHEALASER
6   ILEPHEILEGLYGLNLYSASPTHRSERASN
7   LEUPROLYSGLUTHRVALLYSASNILESER
8   THRTRPGLYALALYSPROLYSLEULYSASP
9   LEUSERASNTYRILELYSTYRTHRLYSASP
10   LYSSERTHRVALTRPVALSERTHRALAILE
11   ASNTHRGLUALAGLYGLYGLNSERSERGLY
12   ALAPROLEUHISLYSILEASPMETASPLEU
13   TYRGLUPHEALAILEASPGLYGLNLYSLEU
14   ASNPROLEUPROGLUGLYARGTHRLYSASN
15   METVALPROSERLEULEULEUASPTHRPRO
16   GLNILEGLUTHRSERSERILEILEALALEU
17   ASNHISGLYPROVALASNASPALAGLUILE
18   SERPHELEUTHRTHRILEPROLEULYSASN
19   VALLYSPROHISLYSARGGLYTHRLEUGLU
20   VALLEUPHEGLN

Samples:

sample_1: TcART, [non-exchangeable-D, U-13C; U-15N], 500 uM; HEPES 20 mM; sodium chloride 150 mM

sample_2: TcART, [U-13C; U-15N], 500 uM; sodium chloride 150 mM; d11-Tris 20 mM

sample_3: TcART, [U-13C; U-15N], 500 uM; HEPES 20 mM; sodium chloride 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.8; pressure: 1 atm; temperature: 280 K

Experiments:

NameSampleSample stateSample conditions
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_3isotropicsample_conditions_1

Software:

TopSpin v3.5pl6, Bruker Biospin - collection, processing

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

ARIA v2.3.2, Linge, O'Donoghue and Nilges - structure calculation

CNS v1.21, Brunger A. T. et.al. - refinement

NMR spectrometers:

  • Bruker AVANCE II 750 MHz
  • Bruker AVANCE III 600 MHz

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