BMRB Entry 34869

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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/BMR34869
MolProbity Validation Chart

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Title:
Solution NMR structure of the peptidyl carrier domain TomAPCP from the Tomaymycin non-ribosomal peptide synthetase in its substrate-loaded state
Deposition date:
2023-10-09
Original release date:
2024-06-20
Authors:
Karanth, M.; Kirkpatrick, J.; Carlomagno, T.
Citation:

Citation: Karanth, M.; Kirkpatrick, J.; Krausze, J.; Schmelz, S.; Carlomagno, T.. "The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain"  Sci. Adv. 10, eadm9404-eadm9404 (2024).
PubMed: 38896613

Assembly members:

Assembly members:
entity_1, polymer, 92 residues, 10483.499 Da.

Natural source:

Natural source:   Common Name: Streptomyces regensis   Taxonomy ID: 68263   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Streptomyces regensis

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPMATAVQNPLETVVLQAWK DISGADDFTTTDSFLGHGGN XLHFVQLASRLQKIFGVEVS TEDVFRHGTVEQLARFVEQS RDTGRNPAAQTQ

Data sets:
Data typeCount
13C chemical shifts603
15N chemical shifts86
1H chemical shifts1121

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 92 residues - 10483.499 Da.

1   GLYPROMETALATHRALAVALGLNASNPRO
2   LEUGLUTHRVALVALLEUGLNALATRPLYS
3   ASPILESERGLYALAASPASPPHETHRTHR
4   THRASPSERPHELEUGLYHISGLYGLYASN
5   WP9LEUHISPHEVALGLNLEUALASERARG
6   LEUGLNLYSILEPHEGLYVALGLUVALSER
7   THRGLUASPVALPHEARGHISGLYTHRVAL
8   GLUGLNLEUALAARGPHEVALGLUGLNSER
9   ARGASPTHRGLYARGASNPROALAALAGLN
10   THRGLN

Samples:

sample_1: TomAPCP substrate-loaded, [U-13C; U-15N], 350 ± 15 uM; sodium phosphate 50 ± 5 mM; sodium chloride 150 ± 15 mM; sodium azide 0.02 ± 0.002 w/v; D2O, [U-2H], 10 ± 0.5 v/v

sample_2: TomAPCP substrate-loaded, [U-13C; U-15N], 500 ± 15 uM; sodium phosphate 50 ± 5 mM; sodium chloride 150 ± 15 mM; sodium azide 0.02 ± 0.002 % w/v; D2O, [U-2H], 100 ± 0.5 v/v

sample_3: TomAPCP substrate-loaded, [U-13C; U-15N], 100 ± 10 uM; sodium phosphate 50 ± 5 mM; sodium chloride 150 ± 15 mM; sodium azide 0.02 ± 0.002 w/v; D2O, [U-2H], 10 ± 0.5 v/v

sample_conditions_1: ionic strength: 265 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

NMRPipe v10.2, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CcpNmr Analysis v2.4, CCPN - chemical shift assignment, data analysis, peak picking

ARIA v2.3, Linge, O'Donoghue and Nilges - structure calculation

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III HD 850 MHz

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