Table 2.
Experimental restraints and structural statistics (for the calculation of the tertiary structure of Bs-CspB in complex with the ssDNA fragment dT7)
| Number of experimental restraints | ||||
| Distance restraints from NOEs | ||||
| Interresidual NOEs | Sequential | (|i − j| = 1) | 283 | |
| Medium long range | (|i − j| < 5) | 135 | ||
| Long range | (|i − j| ≥ 5) | 411 | ||
| Intraresidual NOEs | 381 | |||
| Dihedral angle restraints φ/χ1 | 29/2 | |||
| RDC restraints (DN,HN) | 50 | |||
| Hydrogen bond restriants | 23 | |||
| Molecular dynamics statistics | ||||
| Average energy (kcal/mol) | Etot 31.0 ± 3.0 | |||
| Ebond 0.9 ± 0.1 | ||||
| Eangle 10.2 ± 1.2 | ||||
| Eimproper 2.7 ± 0.6 | ||||
| Evdw 7.6 ± 1.5 | ||||
| ENOE 3.3 ± 1.2 | ||||
| Ecdih 0.1 ± 0.02 | ||||
| ERDC 6.1 ± 1.1 | ||||
| r.m.s.d. from ideal distance (Å) | Bonds 0.00096 ± 0.00007 | |||
| NOE 0.012 ± 0.001 | ||||
| r.m.s.d. from ideal angles (degree) | Bond angles | 0.190 ± 0.012 | ||
| Improper angles | 0.287 ± 0.016 | |||
| r.m.s.d. from dipolar couplings (Hz) | HN-N couplings | 0.071 ± 0.014 | ||
| Atomic r.m.s.d. (Å) of 18 refined Bs-CspB structuresa | ||||
| All residuesb | 0.54 (backbone) | 0.94 (heavy atoms) | ||
| Secondary structurec | 0.21 (backbone) | 0.55 (heavy atoms) | ||
| Pairwise backbone r.m.s.d. (Å) between different Bs-CspB structures | ||||
| NMR(bound)d | X-ray(bound)e | X-ray(free)f | NMR(free)g | |
| NMR(bound) | 0 | 1.44h (0.87)c | 1.34 (0.80) | 1.68 (1.08) |
| X-ray (bound) | — | 0 | 0.92 (0.37) | 1.90 (1.37) |
| X-ray(free) | — | — | 0 | 1.66 (1.28) |
| NMR(free) | — | — | — | 0 |
aThe final force constants used in the structure calculation were 1000 kcal·mol−1·Å−2 for the bond length, 500 kcal·mol−1·rad−2 for the bond angles and improper angles, 50 kcal·mol−1·Å−2 for the NOE distance restraints, 55 kcal·mol−1·rad−2 for the ϕ-angle restraints, and 1.0 kcal·mol−1·Hz−2 for the RDCs.
bCalculated for the final set of 18 structures (residue 1–67).
cCalculated for the elements of regular secondary structure (residues 2–10, 15–19, 26–32, 46–53, 59–65).
dAverage structure from this study.
eCrystal structure of ssDNA-bound Bs-CspB (2ES2.pdb).
fCrystal structure of the free Bs-CspB (1CSP.pdb) (20).
gNMR average structure of the free Bs-CspB(1NMG.pdb) (19).
hCalculated for residues 1–67.