BMRB: 34869Solution NMR structure of the peptidyl carrier domain TomAPCP from the Tomaymycin non-ribosomal peptide synthetase in its substrate-loaded state
Mass: 10483.499 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the ...Details: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the fifth residue has residue-number '1'. A special modified residue SPA is designated for the serine residue covalently linked to a 4'-phosphopantetheine-anthranilate prosthetic group. Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli (E. coli)
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
1
2D 1H-15N HSQC
1
2
3
isotropic
2
2D 1H-13C HSQC
1
3
2
isotropic
2
2D 1H-13C HSQC
1
4
1
isotropic
1
3D 1H-15N NOESY
1
5
2
isotropic
2
3D 1H-13C NOESY
-
Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
solution
1
350 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O, 90% H2O/10% D2O
13C15N_sample
90% H2O/10% D2O
solution
3
100 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O, 90% H2O/10% D2O
13C15N_sample_2
90% H2O/10% D2O
solution
2
500 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 % w/v sodium azide, 100 v/v [U-2H] D2O, 100% D2O
13C15N_D2O_sample
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
350uM
TomAPCP substrate-loaded
[U-13C; U-15N]
1
50mM
sodiumphosphate
naturalabundance
1
150mM
sodiumchloride
naturalabundance
1
0.02w/v
sodiumazide
naturalabundance
1
10v/v
D2O
[U-2H]
1
100uM
TomAPCP substrate-loaded
[U-13C; U-15N]
3
50mM
sodiumphosphate
naturalabundance
3
150mM
sodiumchloride
naturalabundance
3
0.02w/v
sodiumazide
naturalabundance
3
10v/v
D2O
[U-2H]
3
500uM
TomAPCP substrate-loaded
[U-13C; U-15N]
2
50mM
sodiumphosphate
naturalabundance
2
150mM
sodiumchloride
naturalabundance
2
0.02 % w/v
sodiumazide
naturalabundance
2
100v/v
D2O
[U-2H]
2
Sample conditions
Ionic strength: 265 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE III
Bruker
AVANCEIII
600
1
Bruker AVANCE III HD
Bruker
AVANCEIIIHD
850
2
-
Processing
NMR software
Name
Version
Developer
Classification
TopSpin
3.2
BrukerBiospin
collection
NMRPipe
10.2
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
CcpNmr Analysis
2.4
CCPN
peakpicking
CcpNmr Analysis
2.4
CCPN
chemicalshiftassignment
CcpNmr Analysis
2.4
CCPN
dataanalysis
ARIA
2.3
Linge, O'DonoghueandNilges
structurecalculation
CNS
1.21
Brunger, Adams, Clore, Gros, NilgesandRead
structurecalculation
CNS
1.21
Brunger, Adams, Clore, Gros, NilgesandRead
structurecalculation
CNS
1.21
Brunger, Adams, Clore, Gros, NilgesandRead
structurecalculation
Refinement
Method
Software ordinal
simulated annealing
7
torsion angle dynamics
8
molecular dynamics
9
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10
+
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