1W9R
Solution Structure of Choline Binding Protein A, Domain R2, the Major Adhesin of Streptococcus pneumoniae
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D CT-HNCA | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 2 | 3D CT-HNCOCA | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 3 | 3D CT-HNCACB | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 4 | 3D CT- HNCOCACB | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 5 | 4D HNCOCA | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 6 | 4D HNCACO | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 7 | 3D CCONH-TOCSY | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 8 | 3D HCCONH-TOCSY | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 9 | 3D HBHACBCACONH | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 10 | 3D HCCH-COSY | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 11 | 3D HCCH-TOSCY | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 12 | 3D NOESY- 1H-15N HSQC | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 13 | 3D NOESY-1H- 13 CHSQC | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 14 | 4D 1H-15N HSQC- NOESY-1H-15N HSQC | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 15 | 4D 1H- 15N HSQC-NOESY-1H-13C HSQC | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| 16 | 4D 1H-13C HSQC-NOESY-1H- 13C HSQC. | 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V) | APPROX. 60 MM | 6.5 | 1.0 atm | 298.0 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| TAD | A TOTAL OF 2292 NOE INTERPROTON DISTANCE RESTRAINTS, 83 PAIRS OF PSI AND PHI AND BACKBONE DIHEDRAL ANGLE RESTRAINTS, AND 146 PAIRS OF H-BOND RESTRAINTS WERE USED TO CALCULATE AN ENSEMBLE OF STRUCTURES USING A MODIFIED VERSION OF THE ORIGINAL TORSION ANGLE DYNAMICS PROTOCOL ROUTINE WITHIN CNS. THE TAD PROTOCOL WAS AS FOLLOWS. 75 PS HIGH-TEMPERATURE TAD 50000 K FOLLOWED BY COOLING TO 1000 K OVER THE COURSE OF 75 PS AND RAMPING OF THE VAN DER WAALS SCALING TERM FROM 0.1 TO 1.0. THE MOLECULES WERE FURTHER COOLED TO 300 K OVER THE COURSE OF 20 PS USING CONVENTIONAL CARTESIAN DYNAMICS FOLLOWED FINALLY BY 10000 STEPS OF CONJUGATE GRADIENT ENERGY MINIMIZATION. THE NOE ENERGY TERM WAS 150 KCAL PER MOL FOR THE FIRST THREE STEPS AND 100 KCAL PER MOL FOR THE LAST. THE DIHEDRAL RESTRAINT TERM WAS 100 KCAL PER MOL FOR THE FIRST THREE STEPS AND 300 KCAL PER MOL FOR THE LAST. TWO HUNDRED STRUCTURES WERE CALCULATED, AND THE LOWEST 40 STRUCTURES WERE FURTHER REFINED BY USING THE SANDER MODULE OF AMBER 8.0 MOLECULAR MODELING SUITE. THE SOLVENT WAS REPRESENTED BY GENERALIZED-BORN GB SOLVENT MODEL. THE STRUCTURES WERE FIRST ENERGY MINIMIZED FOR1 PS WITHOUT ANY RESTRAINTS FOLLOWED BY 40 PS SIMULATED ANNEALING FROM 400 K TO 0 K WITH ALL THE RESTRAINTS. THE DISTANCE AND ANGLE RESTRAINTS WERE REPRESENTED BY A SQUARE-WELL PENALTY FUNCTION WITH FORCE CONSTANTS OF 20 KCAL PER MOL AND 2 KCAL PER MOL, RESPECTIVELY. | CNS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | LEAST ENERGY |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 19 |
| Additional NMR Experimental Information | |
|---|---|
| Details | CBPA-R2 STRUCTURES WERE CALCULATED USING NMR DATA COLLECTED AT 25 C. INTERPROTON DISTANCES WERE ESTIMATED FROM THE VOLUMES OF CROSS-PEAKS IN 3D AND 4D NOESY SPECTRA. THE RESTRAINT LOWER BOUNDS WERE SET TO THE VAN DER WAALS DISTANCE, AND UPPER BOUNDS WERE SET TO 2.5, 3.5, AND 6.0 FOR STRONG, MEDIUM, AND WEAK RESONANCES, RESPECTIVELY. ESTIMATES OF BACKBONE DIHEDRAL ANGLES F AND Y WERE OBTAINED USING THE PROGRAM TALOS AND 1H , 15N, 13C , 13C , AND 13CO CHEMICAL SHIFT VALUES. TALOS-BASED AND RESTRAINTS WERE USED ONLY WHEN A WELL-DEFINED PREDICTION WAS OBTAINED, AND THIS OCCURRED WITHIN THE HELICAL SEGMENTS OF CBPA-R2. IN ADDITION, H-BOND RESTRAINTS WERE USED WITHIN -HELICES IN THE FOLLOWING WAY. TWO DISTANCE RESTRAINTS WERE USED FOR EACH HYDROGEN BOND, ONE BETWEEN THE HYDROGEN AND THE ACCEPTOR ATOM 1.5-2.3 AND ONE BETWEEN THE DONOR HEAVY ATOM AND THE ACCEPTOR ATOM 2.4-3.3. THESE WERE INTRODUCED AFTER THE INITIAL SET OF STRUCTURE CALCULATIONS. AMIDE PROTONS INVOLVED IN H-BONDS WERE IDENTIFIED ON THE BASIS OF SLOW EXCHANGE WITH D2O. A TOTAL OF 2292 NOE INTERPROTON DISTANCE RESTRAINTS, 83 PAIRS OF AND BACKBONE DIHEDRAL ANGLE RESTRAINTS, AND 146 PAIRS OF H-BOND RESTRAINTS WERE USED TO CALCULATE AN ENSEMBLE OF STRUCTURES USING A MODIFIED VERSION OF THE ORIGINAL TORSION ANGLE DYNAMICS PROTOCOL ROUTINE WITHIN CNS. THE TAD PROTOCOL WAS AS FOLLOWS 75 PS HIGH-TEMPERATURE TAD 50 000 K FOLLOWED BY COOLING TO 1000 K OVER THE COURSE OF 75 PS AND RAMPING OF THE VAN DER WAALS SCALING TERM FROM 0.1 TO 1.0. THE MOLECULES WERE FURTHER COOLED TO 300 K OVER THE COURSE OF 20 PS USING CONVENTIONAL CARTESIAN DYNAMICS FOLLOWED FINALLY BY 10000 STEPS OF CONJUGATE GRADIENT ENERGY MINIMIZATION. THE NOE ENERGY TERM WAS 150 FOR THE FIRST THREE STEPS AND 100 FOR THE LAST. THE DIHEDRAL RESTRAINT TERM WAS 100 FOR THE FIRST THREE STEPS AND 300 FOR THE LAST. TWO HUNDRED STRUCTURES WERE CALCULATED, AND THE LOWEST 40 STRUCTURES WERE FURTHER REFINED BY USING THE SANDER MODULE OF AMBER 8.0 MOLECULAR MODELING SUITE. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CNS | 8.0 | BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARREN |
| 2 | structure solution | CNS | ||
