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Solution structure of two-electron reduced Megasphaera elsdenii flavodoxin
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
COSY
6-10 mM protein, potassium phosphate/potassium pyrophosphate 75-200 mM, pH 8.3, 90% H2O, 10% D2O
90% H2O/10% D2O
8.3
303
2
double quantum filtered COSY
6-10 mM protein, potassium phosphate/potassium pyrophosphate 75-200 mM, pH 8.3, 90% H2O, 10% D2O
90% H2O/10% D2O
8.3
303
3
NOESY (mixing 200ms)
6-10 mM protein, potassium phosphate/potassium pyrophosphate 75-200 mM, pH 8.3, 90% H2O, 10% D2O
90% H2O/10% D2O
8.3
303
4
NOESY (mixing 50, 100, 150 ms)
8.3
303
5
Double Quantum spectra
6-10 mM protein, potassium phosphate/potassium pyrophosphate 75-200 mM, pH 8.3, 90% H2O, 10% D2O
90% H2O/10% D2O
8.3
303
6
Homonuclear Hartmann Hahn transfer spectra
6-10 mM protein, potassium phosphate/potassium pyrophosphate 75-200 mM, pH 8.3, 90% H2O, 10% D2O
90% H2O/10% D2O
8.3
303
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
WM
500
2
Bruker
AM
500
3
Bruker
AM
600
NMR Refinement
Method
Details
Software
restrained molecular dynamics
The Xray structure of the semiquinone state of Clostridium MP flavodoxin was used as a starting structure
for restrained molecular dynamics (RMD) calculations in vacuo (van Mierlo et al. Eur. J. Biochem. 194, 185 - 198 (1990)).
509 distance restraints, 293 medium, 216 long-range were used in refinement. One
repulsive restraint, between N5H of FMN and NH of E60 was included. RMD run was of 120 ps. During the first 50 ps
the force constant was gradually increased to a high value of 4000 kJmol-1nm-2. From 50 ps on, the force constant was kept
constant. The time span of 60-120 ps, at a time resolution of 0.02 ps, was used for calculating
the average structure. The time-averaged (not energy minimised) structure has a potential energy
-2278 +/- 122 kJmol-1, time-averaged sum of all violations is 2.27 nm, largest
occuring violation is 66 pm
DISNMR
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
3000
Conformers Submitted Total Number
1
Representative Model
1 (averaging the restrained molecular dynamics trajectory in the range 60-120 ps.)
Additional NMR Experimental Information
Details
NOESY spectra had mixing times 50, 100, 150 and 200 ms. Double Quantum spectra had a delay of 32 ms. Homonuclear Hartmann Hahn transfer spectra (using MLEV-17 composite pulse cycling) had mixing times 10-160 ms