ID code: 2BPF, PDE011 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 21 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 5 0.089 1 : 2) GA 6 0.104 1 : 3) CA 7 0.082 1 : 4) GA 8 0.191 1 : 5) CA 9 0.139 1 : 6) CA 10 0.220 1 : 7) GA 11 0.065 2 : 1) CB 7 0.220 2 : 2) CB 6 0.096 2 : 3) GB 5 0.127 2 : 4) CB 4 0.048 2 : 5) GB 3 0.133 2 : 6) GB 2 0.229 2 : 7) CB 1 0.151 Strand: 2 Unit: 1 (CB 7) linkage from atom C3' ( 270) to O3' absent Strand= 2 Nucleo= 14 Atoms = 280 Units = 14 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 7 levels ... Strand 1 has 7 bases (5'-3'): GGCGCCG Strand 2 has 7 bases (3'-5'): CCGCGGC FIRST SUM= 29.829 CPTS: 4.691 6.978 2.739 15.420 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 29.829 DEL= 0.000E+00 STEP 2 SUM= 21.510 DEL= -0.832E+01 STEP 3 SUM= 23.767 DEL= 0.226E+01 STEP 4 SUM= 17.847 DEL= -0.592E+01 STEP 5 SUM= 19.925 DEL= 0.208E+01 STEP 6 SUM= 16.420 DEL= -0.350E+01 STEP 7 SUM= 15.108 DEL= -0.131E+01 STEP 8 SUM= 13.970 DEL= -0.114E+01 STEP 9 SUM= 14.643 DEL= 0.673E+00 STEP 10 SUM= 13.530 DEL= -0.111E+01 STEP 11 SUM= 12.815 DEL= -0.715E+00 STEP 12 SUM= 14.458 DEL= 0.164E+01 STEP 13 SUM= 12.649 DEL= -0.181E+01 STEP 14 SUM= 12.397 DEL= -0.251E+00 STEP 15 SUM= 12.013 DEL= -0.384E+00 STEP 16 SUM= 13.775 DEL= 0.176E+01 STEP 17 SUM= 11.955 DEL= -0.182E+01 STEP 18 SUM= 11.860 DEL= -0.951E-01 STEP 19 SUM= 11.728 DEL= -0.132E+00 STEP 20 SUM= 11.599 DEL= -0.129E+00 STEP 21 SUM= 11.423 DEL= -0.176E+00 STEP 22 SUM= 11.278 DEL= -0.145E+00 STEP 23 SUM= 11.217 DEL= -0.611E-01 STEP 24 SUM= 11.166 DEL= -0.510E-01 STEP 25 SUM= 11.128 DEL= -0.378E-01 STEP 26 SUM= 11.096 DEL= -0.322E-01 STEP 27 SUM= 11.077 DEL= -0.196E-01 STEP 28 SUM= 11.067 DEL= -0.943E-02 STEP 29 SUM= 11.068 DEL= 0.127E-02 STEP 30 SUM= 11.065 DEL= -0.323E-02 STEP 31 SUM= 11.065 DEL= -0.268E-03 STEP 32 SUM= 11.065 DEL= -0.190E-05 STEP 33 SUM= 11.065 DEL= -0.132E-04 STEP 34 SUM= 11.065 DEL= -0.578E-05 STEP 35 SUM= 11.065 DEL= -0.391E-05 STEP 36 SUM= 11.065 DEL= -0.304E-05 STEP 37 SUM= 11.065 DEL= -0.154E-05 STEP 38 SUM= 11.065 DEL= -0.150E-05 STEP 39 SUM= 11.065 DEL= -0.118E-05 STEP 40 SUM= 11.065 DEL= -0.373E-06 STEP 41 SUM= 11.065 DEL= -0.925E-08 STEP 42 SUM= 11.065 DEL= -0.145E-08 STEP 43 SUM= 11.065 DEL= -0.416E-12 STEP 44 SUM= 11.065 DEL= 0.000E+00 STEP 45 SUM= 11.065 DEL= 0.178E-14 STEP 46 SUM= 11.065 DEL= -0.178E-14 FINAL SUM= 11.065 CPTS: 3.042 5.472 0.788 1.762 GRA= 0.36E-09 0.11E-08 0.19E-09-0.34E-10 0.70E-10-0.14E-08-0.44E-10 0.31E-10 GRA=-0.39E-09 0.27E-09 0.31E-10 0.17E-09 0.18E-09-0.36E-09-0.18E-09 0.14E-09 GRA=-0.12E-08-0.77E-09-0.11E-09-0.12E-09 0.10E-08 0.12E-09 0.18E-09-0.18E-09 GRA= 0.16E-08 0.12E-08 0.45E-10-0.42E-12 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.412 -0.393 -0.822 P: 4.192 62.509 17.758 D: 1.304 2) U: -0.385 -0.441 -0.811 P: 2.680 60.540 14.585 D: 1.378 3) U: -0.415 -0.408 -0.813 P: 1.868 59.139 11.596 D: 1.806 4) U: -0.514 -0.301 -0.804 P: 0.197 58.258 8.899 D: 2.621 5) U: -0.521 -0.334 -0.786 P: -1.791 57.129 6.517 D: 1.200 6) U: -0.459 -0.348 -0.817 P: -3.449 55.895 3.676 D: 2.757 7) U: -0.387 -0.370 -0.844 P: -4.533 54.875 0.720 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 5 -1.34 1.20 1.33 -4.28 1 0 2) GA 6 -1.03 0.85 -2.90 -4.05 1 5 3) CA 7 -1.61 0.57 2.18 -0.72 3 -13 4) GA 8 -1.26 0.58 4.65 -1.97 1 13 5) CA 9 -1.71 0.27 9.09 -5.48 3 -5 6) CA 10 -0.98 0.23 7.54 -10.49 3 -9 7) GA 11 -0.87 0.27 15.29 0.72 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 7 -1.47 -1.01 -7.45 6.45 3 0 2) CB 6 -1.15 -1.05 1.92 -3.20 3 -5 3) GB 5 -1.32 -0.81 4.30 -4.03 1 13 4) CB 4 -1.11 -1.06 -3.49 -8.28 3 -13 5) GB 3 -0.05 -0.44 -0.65 -8.98 1 5 6) GB 2 -0.58 -0.38 5.23 -8.71 1 9 7) CB 1 0.06 -0.66 -8.70 5.46 3 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 5-C 7 -1.40 1.10 -3.06 -5.37 1 0 2) G 6-C 6 -1.09 0.95 -0.49 -0.43 1 5 3) C 7-G 5 -1.46 0.69 3.24 1.66 3 -13 4) G 8-C 4 -1.19 0.82 0.58 3.16 1 13 5) C 9-G 3 -0.88 0.36 4.22 1.75 3 -5 6) C 10-G 2 -0.78 0.31 6.38 -0.89 3 -9 7) G 11-C 1 -0.41 0.47 3.30 -2.37 1 0 Average: -1.03 0.67 2.02 -0.36 --------------------------------- |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 5-C 7 0.12 0.19 0.16 8.78 2.17 2.79 1 0 2) G 6-C 6 0.12 -0.20 -0.70 -4.82 -7.25 -5.59 1 5 3) C 7-G 5 -0.29 -0.24 -0.62 -2.12 -4.75 -7.03 3 -13 4) G 8-C 4 -0.15 -0.47 0.58 8.14 -10.25 -12.62 1 13 5) C 9-G 3 -1.65 -0.17 -0.38 9.74 -14.46 -2.78 3 -5 6) C 10-G 2 -0.40 -0.15 -0.09 2.31 -19.20 -2.64 3 -9 7) G 11-C 1 -0.93 -0.39 0.68 23.99 6.19 -5.37 1 0 Average: -0.45 -0.20 -0.05 6.57 -6.79 -4.75 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 5/G 6 0.56 -0.56 3.59 -1.62 2.11 26.45 1 3) G 6/C 7 -1.12 -0.51 3.39 2.60 3.79 30.45 5 4) C 7/G 8 0.50 0.29 3.89 -3.33 4.81 30.64 8 5) G 8/C 9 -0.22 -0.62 2.80 6.56 -4.08 31.92 5 6) C 9/C 10 0.67 0.02 3.66 -5.13 -6.88 44.13 -1 7) C 10/G 11 0.40 0.33 3.67 3.14 11.43 29.04 8 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 7/C 6 0.57 0.16 4.45 11.98 -11.54 34.84 -1 3) C 6/G 5 -0.71 0.47 3.31 -0.11 -1.29 31.88 5 4) G 5/C 4 0.35 -0.53 2.68 -13.58 -10.31 36.23 8 5) C 4/G 3 1.28 0.92 3.76 4.96 -0.13 22.08 5 6) G 3/G 2 -0.58 0.00 3.37 2.30 2.15 43.98 1 7) G 2/C 1 0.93 -0.58 2.90 -18.54 13.95 31.77 8 --------------------------------------- |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 5/G 6 0.56 -0.36 4.02 5.18 6.83 30.65 1 3) G 6/C 7 -0.92 -0.49 3.35 1.24 2.54 31.16 5 4) C 7/G 8 0.42 0.41 3.29 -8.46 7.56 33.43 8 5) G 8/C 9 0.53 -0.77 3.28 5.76 -1.97 27.00 5 6) C 9/C 10 0.05 0.01 3.52 -1.41 -4.52 44.06 -1 7) C 10/G 11 0.66 0.45 3.29 -7.70 -1.26 30.41 8 Average: 0.22 -0.12 3.46 -0.90 1.53 32.79 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 5/G 6 0.37 -1.13 3.64 0.38 1.78 26.51 1 3) G 6/C 7 -1.37 -1.28 3.39 3.65 3.34 30.34 5 4) C 7/G 8 0.22 -0.21 3.97 -3.21 6.13 30.30 8 5) G 8/C 9 -0.26 -1.05 2.98 8.45 -0.03 31.32 5 6) C 9/C 10 0.93 -0.44 3.61 1.03 -0.36 44.22 -1 7) C 10/G 11 0.49 0.50 3.63 5.38 16.59 28.40 8 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 7/C 6 -0.06 -1.28 4.50 12.62 9.30 34.86 -1 3) C 6/G 5 -1.44 -0.93 3.24 -2.15 3.10 31.73 5 4) G 5/C 4 -0.43 -0.26 2.74 -16.53 10.69 34.98 8 5) C 4/G 3 0.38 -1.28 3.85 1.52 -0.81 22.53 5 6) G 3/G 2 -1.38 -0.10 3.17 -4.79 -0.33 43.79 1 7) G 2/C 1 0.65 0.40 2.91 -19.17 -13.82 31.90 8 -------------------------------------- |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 5/G 6 0.17 -1.20 4.06 6.43 5.66 30.55 1 3) G 6/C 7 -1.42 -1.10 3.31 0.76 3.06 31.06 5 4) C 7/G 8 -0.14 -0.29 3.36 -10.03 7.83 32.59 8 5) G 8/C 9 0.12 -1.10 3.35 5.03 -0.60 27.00 5 6) C 9/C 10 -0.26 -0.31 3.51 -1.90 -0.43 44.44 -1 7) C 10/G 11 0.56 0.43 3.21 -6.18 0.76 31.39 8 Average: -0.16 -0.60 3.47 -0.98 2.71 32.84 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 5/G 6 0.25 -0.21 2.61 1.89 0.33 3.22 4.03 1 3) G 6/C 7 -0.54 -0.23 -2.49 0.46 0.59 2.53 3.40 5 4) C 7/G 8 0.15 0.29 -5.80 6.06 0.32 8.38 3.29 8 5) G 8/C 9 0.22 -0.31 2.12 -0.57 0.38 2.20 3.30 5 6) C 9/C 10 -0.05 0.05 -3.58 -1.87 0.08 4.04 3.51 -1 7) C 10/G 11 0.29 0.29 -4.61 0.22 0.41 4.62 3.31 8 Overall axis bend ... UU= 2.33 PP= 12.32 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 5 0.00 0.00 2) G 6 0.54 122.73 3) C 7 1.02 56.71 4) G 8 0.60 18.51 5) C 9 0.35 76.24 6) C 10 0.44 57.55 7) G 11 0.00 0.00 Path length= 20.85 End-to-end= 20.61 Shortening= 1.14 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 5 48.06 -24.94 119.17 53.55 C1'-exo 101.6 98.7 104.4 2)GA 6 35.78 -40.23 174.49 41.37 C2'-endo 106.1 99.7 102.5 3)CA 7 22.87 -25.08 172.35 25.84 C2'-endo 107.4 103.6 104.7 4)GA 8 8.72 -8.99 166.28 9.44 C2'-endo 108.1 105.1 106.6 5)CA 9 34.91 -6.20 97.32 53.63 O1'-endo 101.7 100.4 104.5 6)CA 10 11.17 13.83 70.91 41.99 C4'-exo 106.3 103.2 104.1 7)GA 11 46.68 -43.11 157.13 48.14 C2'-endo 104.0 97.0 102.1 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 5 -101.99 51.23 119.27 164.51 -94.36 -68.78 -166.80 2)GA 6 -107.35 56.05 151.15 -153.72 -142.30 -47.64 -173.50 3)CA 7 -102.62 29.34 143.15 -173.75 -82.57 -99.38 174.28 4)GA 8 -115.17 82.03 117.99 -176.61 -91.44 -77.59 -179.63 5)CA 9 -131.05 73.19 107.96 -175.90 -84.34 -92.32 155.72 6)CA 10 -142.97 91.69 91.84 -138.24 -75.34 -59.36 177.11 7)GA 11 -82.88 39.55 148.54 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 7 -39.26 52.10 8.53 54.05 C3'-endo 106.5 96.6 97.8 2)CB 6 23.03 -6.98 104.22 30.21 O1'-endo 107.3 104.8 104.5 3)GB 5 50.44 -37.18 136.50 51.95 C1'-exo 98.4 99.0 103.4 4)CB 4 10.34 13.03 70.37 39.56 C4'-exo 105.5 104.0 103.6 5)GB 3 27.72 -37.73 189.69 39.19 C3'-exo 107.1 101.0 101.9 6)GB 2 -17.94 34.28 27.63 39.23 C3'-endo 107.5 102.3 103.1 7)CB 1 21.54 -2.93 95.55 33.28 O1'-endo 105.9 105.1 104.4 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 7 -137.19 11.62 ...... ...... ...... ...... ...... 2)CB 6 -125.26 60.76 105.26 -173.50 -91.29 -46.15 -176.35 3)GB 5 -89.76 60.52 135.73 173.76 -96.13 -63.53 179.02 4)CB 4 -144.63 71.25 92.18 -177.17 -55.01 -92.44 -172.62 5)GB 3 -116.60 47.81 151.65 -157.02 -114.17 -79.81 161.50 6)GB 2 -138.15 -177.22 99.11 -162.20 -47.95 -78.45 -161.77 7)CB 1 -171.86 134.01 106.64 -73.73 168.51 61.31 -96.68