ID code: 1LV5, PD0317 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 17 May 24 * *********************************** ************** FILE : duplex.pdb lis : dna : axin : axout: daf : pdb : acc : 0.000 wid : 0.750 maxn : 500 ior : 0 ibond: 0 splin: 3 break: -1 NLEVE: 0 NBAC : 7 ends : F supp : T COMB : T dinu : F mini : T rest : F LINE : F zaxe : F FIT : T test : F GRV : F old : T axonl: F Least squares fitting of standard bases ... Str Pos Base Rms (ang) 1 : 1) GA 20 0.020 1 : 2) GA 21 0.020 1 : 3) AA 22 0.015 1 : 4) TA 23 0.018 1 : 5) CA 24 0.020 1 : 6) AA 25 0.016 1 : 7) GA 26 0.020 1 : 8) CA 27 0.035 1 : 9) GA 28 0.037 1 : 10) AA 29 0.016 2 : 1) CB 13 0.013 2 : 2) CB 12 0.018 2 : 3) TB 11 0.032 2 : 4) AB 10 0.015 2 : 5) GB 9 0.019 2 : 6) TB 8 0.017 2 : 7) CB 7 0.032 2 : 8) GB 6 0.018 2 : 9) CB 5 0.012 2 : 10) TB 4 0.019 Strand: 1 Unit: 10 (AA 29) linkage from atom C3' ( 193) to O3' absent Strand= 2 Nucleo= 20 Atoms = 406 Units = 20 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 10 levels ... Strand 1 has 10 bases (5'-3'): GGATCAGCGA Strand 2 has 10 bases (3'-5'): CCTAGTCGCT FIRST SUM= 54.215 CPTS: 7.125 7.822 7.967 31.300 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 40 STEP 1 SUM= 54.215 DEL= 0.000E+00 STEP 2 SUM= 39.688 DEL= -0.145E+02 STEP 3 SUM= 70.440 DEL= 0.308E+02 STEP 4 SUM= 36.159 DEL= -0.343E+02 STEP 5 SUM= 31.405 DEL= -0.475E+01 STEP 6 SUM= 27.487 DEL= -0.392E+01 STEP 7 SUM= 26.905 DEL= -0.582E+00 STEP 8 SUM= 25.370 DEL= -0.154E+01 STEP 9 SUM= 23.893 DEL= -0.148E+01 STEP 10 SUM= 22.888 DEL= -0.100E+01 STEP 11 SUM= 22.247 DEL= -0.641E+00 STEP 12 SUM= 21.391 DEL= -0.856E+00 STEP 13 SUM= 20.395 DEL= -0.996E+00 STEP 14 SUM= 22.325 DEL= 0.193E+01 STEP 15 SUM= 20.142 DEL= -0.218E+01 STEP 16 SUM= 19.717 DEL= -0.424E+00 STEP 17 SUM= 19.479 DEL= -0.238E+00 STEP 18 SUM= 20.049 DEL= 0.570E+00 STEP 19 SUM= 19.425 DEL= -0.624E+00 STEP 20 SUM= 19.346 DEL= -0.791E-01 STEP 21 SUM= 19.213 DEL= -0.133E+00 STEP 22 SUM= 19.046 DEL= -0.167E+00 STEP 23 SUM= 19.199 DEL= 0.153E+00 STEP 24 SUM= 18.989 DEL= -0.210E+00 STEP 25 SUM= 18.917 DEL= -0.719E-01 STEP 26 SUM= 18.837 DEL= -0.799E-01 STEP 27 SUM= 18.744 DEL= -0.932E-01 STEP 28 SUM= 18.689 DEL= -0.555E-01 STEP 29 SUM= 18.645 DEL= -0.442E-01 STEP 30 SUM= 18.590 DEL= -0.548E-01 STEP 31 SUM= 18.561 DEL= -0.292E-01 STEP 32 SUM= 18.537 DEL= -0.236E-01 STEP 33 SUM= 18.530 DEL= -0.726E-02 STEP 34 SUM= 18.522 DEL= -0.762E-02 STEP 35 SUM= 18.518 DEL= -0.387E-02 STEP 36 SUM= 18.517 DEL= -0.100E-02 STEP 37 SUM= 18.517 DEL= -0.267E-03 STEP 38 SUM= 18.517 DEL= -0.682E-04 STEP 39 SUM= 18.517 DEL= -0.451E-04 STEP 40 SUM= 18.517 DEL= -0.164E-04 STEP 41 SUM= 18.517 DEL= -0.249E-04 STEP 42 SUM= 18.517 DEL= -0.266E-04 STEP 43 SUM= 18.517 DEL= -0.465E-05 STEP 44 SUM= 18.517 DEL= -0.955E-06 STEP 45 SUM= 18.517 DEL= -0.740E-06 STEP 46 SUM= 18.517 DEL= -0.247E-06 STEP 47 SUM= 18.517 DEL= -0.999E-07 STEP 48 SUM= 18.517 DEL= -0.217E-07 STEP 49 SUM= 18.517 DEL= -0.756E-08 STEP 50 SUM= 18.517 DEL= -0.933E-09 STEP 51 SUM= 18.517 DEL= -0.774E-10 STEP 52 SUM= 18.517 DEL= -0.180E-10 STEP 53 SUM= 18.517 DEL= -0.192E-12 STEP 54 SUM= 18.517 DEL= 0.355E-14 STEP 55 SUM= 18.517 DEL= -0.355E-14 FINAL SUM= 18.517 CPTS: 4.635 8.526 2.643 2.713 GRA=-0.32E-08 0.25E-08 0.28E-09 0.43E-08-0.53E-08-0.51E-10-0.15E-08-0.50E-08 GRA=-0.53E-08-0.31E-08 0.32E-09-0.42E-08 0.33E-08 0.12E-07 0.27E-08 0.66E-08 GRA=-0.73E-08 0.24E-08-0.44E-09-0.67E-09 0.27E-08 0.42E-08-0.59E-08-0.20E-08 GRA=-0.46E-08 0.77E-08 0.35E-08 0.31E-08 0.41E-08 0.16E-08 0.14E-08-0.11E-09 GRA= 0.40E-08 0.69E-08-0.92E-09 0.19E-08 0.44E-08 0.39E-08-0.27E-09 0.19E-08 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.074 0.994 -0.083 P: 1.631 19.412 -82.749 D: 3.310 2) U: 0.082 0.987 -0.137 P: 1.098 22.855 -83.029 D: 5.336 3) U: 0.135 0.991 -0.013 P: 2.058 25.813 -83.830 D: 1.072 4) U: 0.109 0.994 0.022 P: 2.457 28.987 -83.824 D: 1.834 5) U: 0.090 0.995 0.047 P: 2.836 32.537 -83.658 D: 1.324 6) U: 0.181 0.976 0.118 P: 3.378 36.120 -83.328 D: 1.436 7) U: 0.230 0.958 0.169 P: 3.976 38.876 -82.712 D: 0.788 8) U: 0.317 0.942 0.111 P: 4.829 42.123 -82.279 D: 2.965 9) U: 0.422 0.904 -0.074 P: 6.458 45.221 -81.892 D: 0.452 10) U: 0.496 0.865 -0.078 P: 8.176 48.231 -82.274 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 20 -0.73 -0.84 -2.38 -9.72 1 0 2) GA 21 0.04 -0.02 1.78 -2.75 1 2 3) AA 22 -0.97 -0.04 4.82 -7.89 2 22 4) TA 23 -1.65 0.03 6.60 -11.56 4 -22 5) CA 24 -1.04 0.13 7.60 -9.11 3 -12 6) AA 25 -1.39 -0.31 -2.81 -6.85 2 25 7) GA 26 -1.76 -0.49 9.03 0.78 1 7 8) CA 27 -2.04 -0.26 5.63 -2.97 3 -13 9) GA 28 -2.31 -0.75 -1.30 1.49 1 10 10) AA 29 -2.36 -0.85 1.71 -2.31 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 13 0.17 0.64 0.83 -12.53 3 0 2) CB 12 0.37 0.97 2.81 0.28 3 -2 3) TB 11 -0.75 0.44 -5.32 -13.99 4 -22 4) AB 10 -0.55 0.44 -2.25 -9.66 2 22 5) GB 9 -1.58 0.75 1.32 0.10 1 12 6) TB 8 -1.66 0.43 9.33 -4.52 4 -25 7) CB 7 -1.74 0.54 -1.36 1.31 3 -7 8) GB 6 -1.87 0.60 -5.02 -7.15 1 13 9) CB 5 -2.12 1.14 -2.98 -15.67 3 -10 10) TB 4 -1.89 1.32 -1.23 -17.61 4 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) G 20-C 13 -0.28 -0.74 -0.77 1.41 1 0 2) G 21-C 12 0.20 -0.49 2.29 -1.51 1 2 3) A 22-T 11 -0.86 -0.24 -0.25 3.05 2 22 4) T 23-A 10 -1.10 -0.20 2.18 -0.95 4 -22 5) C 24-G 9 -1.31 -0.31 4.46 -4.60 3 -12 6) A 25-T 8 -1.52 -0.37 3.26 -1.17 2 25 7) G 26-C 7 -1.75 -0.51 3.83 -0.27 1 7 8) C 27-G 6 -1.95 -0.43 0.30 2.09 3 -13 9) G 28-C 5 -2.22 -0.95 -2.14 8.58 1 10 10) A 29-T 4 -2.13 -1.09 0.24 7.65 2 0 Average: -1.29 -0.53 1.34 1.43 --------------------------------- |D| Global Base-Base Parameters | --------------------------------- Strand 1 with strand 2 ... Duplex Shear Stretch Stagger Buckle Propel Opening Bc Tc (Sx) (Sy) (Sz) (kappa) (omega) (sigma) 1) G 20-C 13 -0.90 -0.21 -0.03 -3.21 -22.25 -2.09 1 0 2) G 21-C 12 -0.32 0.95 -0.02 -1.03 -2.47 19.16 1 2 3) A 22-T 11 -0.21 0.40 0.22 10.14 -21.88 11.83 2 22 4) T 23-A 10 -1.10 0.47 -0.64 8.85 -21.22 12.66 4 -22 5) C 24-G 9 0.55 0.87 -0.45 6.28 -9.01 8.60 3 -12 6) A 25-T 8 0.27 0.12 -0.66 -12.14 -11.37 5.93 2 25 7) G 26-C 7 -0.02 0.05 -0.45 10.39 2.09 -2.41 1 7 8) C 27-G 6 -0.17 0.34 -0.96 10.65 -10.13 3.95 3 -13 9) G 28-C 5 -0.19 0.39 -0.15 1.67 -14.18 5.83 1 10 10) A 29-T 4 -0.47 0.47 -0.66 2.94 -19.92 11.07 2 0 Average: -0.26 0.39 -0.38 3.45 -13.03 7.45 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 20/G 21 1.33 0.86 3.47 6.21 -2.25 55.10 1 3) G 21/A 22 -1.86 0.01 3.22 -4.15 -2.32 28.16 2 4) A 22/T 23 -0.69 0.08 2.77 2.78 -1.39 35.07 7 5) T 23/C 24 0.66 0.10 3.67 2.57 3.34 34.58 -2 6) C 24/A 25 -0.29 -0.44 3.54 -9.72 8.94 32.33 9 7) A 25/G 26 -0.36 -0.38 2.98 14.73 10.63 21.53 3 8) G 26/C 27 -0.33 0.30 3.13 -3.63 2.33 41.35 5 9) C 27/G 28 -0.40 -0.96 3.92 -6.08 16.82 25.21 8 10) G 28/A 29 0.07 -0.24 3.23 7.82 -3.51 32.27 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 13/C 12 0.76 0.30 3.46 4.04 22.03 33.85 -1 3) C 12/T 11 -1.97 -0.56 2.98 -15.32 -17.10 35.49 -2 4) T 11/A 10 0.19 -0.01 3.63 4.07 2.05 34.24 7 5) A 10/G 9 -0.98 0.30 3.47 5.14 8.87 38.64 2 6) G 9/T 8 -0.02 -0.31 3.75 8.69 -11.30 34.99 -9 7) T 8/C 7 -0.06 0.31 2.78 -7.79 2.83 29.87 -3 8) C 7/G 6 -0.18 -0.01 3.64 -3.89 -14.55 35.00 5 9) G 6/C 5 -0.37 1.01 3.10 2.90 -20.88 23.33 8 10) C 5/T 4 0.35 0.32 3.74 6.55 -2.23 27.02 -2 --------------------------------------- |F| Global Inter-Base pair Parameters | --------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 20/G 21 1.04 0.28 3.46 5.13 -12.14 44.47 1 3) G 21/A 22 -1.92 0.29 3.10 -9.73 7.39 31.83 2 4) A 22/T 23 -0.25 0.05 3.20 3.43 -1.72 34.66 7 5) T 23/C 24 -0.16 -0.10 3.57 3.86 -2.76 36.61 -2 6) C 24/A 25 -0.15 -0.06 3.65 -0.52 10.12 33.66 9 7) A 25/G 26 -0.21 -0.35 2.88 3.47 3.90 25.70 3 8) G 26/C 27 -0.25 0.16 3.39 -3.76 8.44 38.18 5 9) C 27/G 28 -0.38 -0.98 3.51 -1.59 18.85 24.27 8 10) G 28/A 29 0.21 -0.28 3.48 7.19 -0.64 29.64 2 Average: -0.23 -0.11 3.36 0.83 3.49 33.22 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 20/G 21 1.91 0.29 3.25 10.75 -3.44 54.16 1 3) G 21/A 22 -1.52 0.12 3.40 -1.22 0.38 28.06 2 4) A 22/T 23 -0.20 -0.41 2.94 8.67 2.08 33.73 7 5) T 23/C 24 1.21 -0.28 3.61 8.65 7.27 33.31 -2 6) C 24/A 25 0.33 -0.97 3.71 -4.44 10.11 33.08 9 7) A 25/G 26 -0.12 -0.83 3.13 15.84 11.44 20.81 3 8) G 26/C 27 0.02 -0.61 3.44 -2.62 7.68 40.28 5 9) C 27/G 28 -0.14 -1.76 4.44 -5.16 17.59 24.96 8 10) G 28/A 29 0.51 -1.48 3.19 7.95 -3.58 32.28 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 13/C 12 0.83 0.14 3.62 1.04 -20.21 34.88 -1 3) C 12/T 11 -1.77 0.09 3.02 -19.66 14.32 34.06 -2 4) T 11/A 10 -0.30 -0.57 3.65 -3.33 -3.99 34.40 7 5) A 10/G 9 -0.83 -0.93 3.44 1.68 -8.47 39.05 2 6) G 9/T 8 0.14 -0.37 4.02 6.68 14.26 34.75 -9 7) T 8/C 7 0.19 -0.97 2.93 -8.29 -0.53 29.41 -3 8) C 7/G 6 0.06 -1.35 3.76 -5.58 12.20 35.25 5 9) G 6/C 5 -0.59 -2.10 3.32 -2.53 19.06 24.35 8 10) C 5/T 4 -0.13 -1.40 3.72 -1.47 1.54 27.76 -2 -------------------------------------- |H| Local Inter-Base pair Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 20/G 21 1.37 0.25 3.44 5.30 -11.45 44.41 1 3) G 21/A 22 -1.64 0.11 3.18 -9.31 8.60 30.70 2 4) A 22/T 23 -0.18 -0.45 3.25 2.36 -0.25 34.79 7 5) T 23/C 24 0.15 -0.51 3.63 4.44 -0.24 36.90 -2 6) C 24/A 25 0.27 -0.66 3.85 1.25 11.83 34.02 9 7) A 25/G 26 0.03 -0.90 3.00 3.63 5.70 24.91 3 8) G 26/C 27 0.05 -0.96 3.62 -4.08 10.00 37.39 5 9) C 27/G 28 -0.42 -1.94 3.89 -3.82 18.25 24.72 8 10) G 28/A 29 0.23 -1.41 3.48 3.46 -0.65 30.31 2 Average: -0.02 -0.72 3.48 0.36 4.64 33.13 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 20/G 21 0.56 0.04 2.06 -9.22 0.56 9.45 3.50 1 3) G 21/A 22 -0.85 0.03 -7.19 2.83 0.85 7.73 3.21 2 4) A 22/T 23 -0.01 0.01 1.00 2.28 0.01 2.48 3.20 7 5) T 23/C 24 0.05 0.00 1.58 0.89 0.05 1.81 3.57 -2 6) C 24/A 25 0.06 -0.00 0.69 6.68 0.06 6.72 3.64 9 7) A 25/G 26 0.02 -0.21 2.89 3.00 0.21 4.17 2.89 3 8) G 26/C 27 -0.05 0.08 -0.23 6.08 0.09 6.08 3.39 5 9) C 27/G 28 -0.12 -0.47 0.86 12.37 0.48 12.40 3.52 8 10) G 28/A 29 0.12 -0.14 4.80 0.29 0.18 4.81 3.49 2 Overall axis bend ... UU= 33.98 PP= 38.37 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 20 0.00 0.00 2) G 21 1.32 127.22 3) A 22 1.55 64.23 4) T 23 1.80 35.83 5) C 24 2.06 11.42 6) A 25 2.17 -11.65 7) G 26 2.04 -18.31 8) C 27 1.91 -49.38 9) G 28 1.10 -54.89 10) A 29 0.00 0.00 Path length= 30.40 End-to-end= 29.56 Shortening= 2.77 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 20 28.52 -29.56 167.25 30.84 C2'-endo 105.9 104.0 103.6 2)GA 21 34.13 -32.75 160.76 35.51 C2'-endo 105.9 102.1 103.4 3)AA 22 32.97 -31.80 160.97 34.37 C2'-endo 106.0 102.5 103.7 4)TA 23 32.97 -30.88 158.67 33.94 C2'-endo 106.0 102.7 103.5 5)CA 24 34.72 -30.80 154.21 35.13 C2'-endo 105.8 102.4 103.3 6)AA 25 -6.18 24.53 45.19 35.50 C4'-exo 107.7 104.7 102.6 7)GA 26 37.87 -34.88 157.45 38.82 C2'-endo 106.1 100.7 103.5 8)CA 27 -21.16 35.57 22.32 39.18 C3'-endo 107.4 102.3 102.0 9)GA 28 -21.59 34.40 19.61 37.16 C3'-endo 106.8 103.3 101.9 10)AA 29 -22.25 32.44 14.32 34.08 C3'-endo 107.1 103.3 102.8 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 20 -161.40 175.85 141.56 -152.05 -69.65 -77.84 174.67 2)GA 21 -95.29 51.59 141.89 -152.05 -153.82 -56.93 149.29 3)AA 22 -112.95 53.37 139.97 -164.84 -114.46 -62.38 173.60 4)TA 23 -100.31 47.47 136.27 -176.18 -94.82 -56.88 -173.12 5)CA 24 -89.66 41.03 135.19 -173.27 -117.17 -62.50 157.59 6)AA 25 -142.85 55.48 85.48 -176.02 -62.60 -68.64 -166.22 7)GA 26 -92.72 50.44 143.17 -159.77 -128.33 -84.22 159.60 8)CA 27 -143.10 47.17 79.97 -160.97 -75.63 -64.86 178.19 9)GA 28 -158.16 53.38 82.12 -171.21 -69.39 -60.55 177.32 10)AA 29 -152.36 55.81 ...... ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 13 -20.30 31.19 17.81 33.42 C3'-endo 107.1 103.7 102.6 2)CB 12 34.16 -32.44 159.97 35.37 C2'-endo 105.9 102.2 103.5 3)TB 11 -18.28 29.73 20.95 32.46 C3'-endo 107.3 103.9 102.8 4)AB 10 -8.75 26.59 41.09 35.99 C4'-exo 107.6 104.5 102.4 5)GB 9 32.66 -31.28 160.50 33.92 C2'-endo 105.8 102.9 103.4 6)TB 8 34.03 -31.43 157.16 34.88 C2'-endo 105.6 102.4 103.6 7)CB 7 29.89 -29.80 163.89 31.63 C2'-endo 105.9 103.5 103.5 8)GB 6 -15.36 28.41 27.08 32.56 C3'-endo 107.4 104.2 102.7 9)CB 5 -20.35 34.39 22.47 37.96 C3'-endo 107.4 102.4 102.5 10)TB 4 -17.88 30.33 23.07 33.63 C3'-endo 107.5 103.8 102.7 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 13 -147.27 56.92 89.72 ...... ...... ...... ...... 2)CB 12 -96.95 56.96 141.73 -166.96 -157.32 -54.03 136.19 3)TB 11 -146.88 57.93 88.92 -155.52 -59.60 -59.52 177.82 4)AB 10 -146.30 53.44 83.46 -166.46 -85.82 -56.23 160.83 5)GB 9 -109.95 40.38 137.94 -169.31 -112.38 -57.85 154.97 6)TB 8 -99.46 42.35 136.12 -162.58 -125.63 -49.54 165.48 7)CB 7 -113.13 46.67 136.88 178.41 -93.08 -60.76 -171.59 8)GB 6 -173.06 -173.25 88.15 -147.34 -65.48 -59.97 -169.63 9)CB 5 -147.59 45.56 79.18 -161.47 -84.31 147.02 -148.14 10)TB 4 -147.42 50.69 86.83 -163.77 -69.54 -56.81 174.28