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SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS THERMOPHILUS
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
HNCA
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
2
HN(CO)CA
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
3
CBCANH
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
4
CBCA(CO)NH
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
5
C(CO)NH-TOCSY
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
6
HCCH-TOCSY
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
7
(HB)CB(CGCD)HD
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
8
(HB)CB(CGCDCE)HE
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
9
15N-EDITED NOESY-HSQC
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
10
15N-EDITED TOCSY-HSQC
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
11
3D HNHA
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
12
2D NOESY
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
13
2D TOCSY
90% WATER/10% D2O
0.250 M
6.5
1 atm
303
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
INOVA
500
2
Varian
INOVA
600
3
Varian
INOVA
800
NMR Refinement
Method
Details
Software
simulated annealing
THE STRUCTURE WAS DETERMINED USING 1104 DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 14 HYDROGEN BOND RESTRAINTS. 50 STRUCTURES WERE CALCULATED AND REFINED USING AN AB INITIO SIMULATED ANNEALING PROTOCOL FOR X- PLOR AND THEN REFINED IN TWO STEPS. AN R-6 AVERAGING PROTOCOL WAS USED FOR NON-STEREOSPECIFICALLY ASSIGNED PROTONS [1]. DURING THE SIMULATED ANNEALING STEP AND THE FIRST REFINEMENT STEP ONLY THE REPULSIVE PART OF THE VAN DER WAALS INTERACTION WAS INCLUDED. IN THE SECOND REFINEMENT STEP THE VAN DER WAALS INTERACTION WAS PARAMETERIZED USING A LENNARD-JONES POTENTIAL INCLUDING THE ATTRACTIVE PART. 21 STRUCTURES WERE SELECTED ON THE BASIS OF CUMULATIVE RMSD VALUES OF STRUCTURES, ORDERED AFTER OVERALL ENERGY, AND RAMACHANDRAN BEHAVIOR FOR REGIONS WITH LOW RESTRAINT DENSITIES. [1] BRUNGER, A. T., CLORE, G. M., GRONENBORN, A. M. & KARPLUS, M. (1986). THREE-DIMENSIONAL STRUCTURE OF PROTEINS DETERMINED BY MOLECULAR DYNAMICS WITH INTERPROTON DISTANCE RESTRAINTS: APPLICATION TO CRAMBIN. PROC NATL ACAD SCI USA 83, 3801-3805. OTHER DETAILS OF STRUCTURE REFINEMENT CAN BE FOUND IN THE JRNL CITATION.
X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
CUMULATIVE RMSD OF STRUCTURES SORTED AFTER TOTAL ENERGY
Conformers Calculated Total Number
50
Conformers Submitted Total Number
21
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
refinement
X-PLOR
3.851
BRUNGER STRUCTURAL STATISTICS: 21 SA STRUCTURES SAAVEMIN[A] RMS DEVIATIONS FROM EXP. RESTRAINTS NOE DISTANCE RESTRAINTS (1104) 0.036 A 0.032 A DIHEDRAL ANGLE RESTRAINTS (42) 0.380 DEG 0.380 DEG DEVIATIONS FROM IDEAL GEOMETRY BONDS 0.0045 A 0.0041 A ANGLES 0.71 DEG 0.66 DEG IMPROPERS 0.54 DEG 0.49 DEG