**************************************************************************** File name: 5iim.pdb no. of DNA/RNA chains: 3 [D=4,P=6,T=11] no. of nucleotides: 22 no. of atoms: 3290 no. of waters: 349 no. of metals: 2 [Na=2] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 8OG-g 1 T.8OG6 2 DUP-u 1 A.DUP601 **************************************************************************** List of 11 base pairs nt1 nt2 bp name Saenger LW DSSR 1 D.DG1 T.DC4 G-C WC 19-XIX cWW cW-W 2 D.DC2 T.DG3 C-G WC 19-XIX cWW cW-W 3 D.DC3 T.DG2 C-G WC 19-XIX cWW cW-W 4 D.DG4 T.DC1 G-C WC 19-XIX cWW cW-W 5 P.DC1 T.DG11 C-G WC 19-XIX cWW cW-W 6 P.DA2 T.DT10 A-T WC 20-XX cWW cW-W 7 P.DG3 T.DC9 G-C WC 19-XIX cWW cW-W 8 P.DT4 T.DA8 T-A WC 20-XX cWW cW-W 9 P.DA5 T.DT7 A-T WC 20-XX cWW cW-W 10 P.DA6 T.8OG6 A+g -- 09-IX cWH cW+M 11 T.DA5 A.DUP601 A-u WC 20-XX cWW cW-W **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[1] bps=4 strand-1 5'-GCCG-3' bp-type |||| strand-2 3'-CGGC-5' helix-form .BB 1 D.DG1 T.DC4 G-C WC 19-XIX cWW cW-W 2 D.DC2 T.DG3 C-G WC 19-XIX cWW cW-W 3 D.DC3 T.DG2 C-G WC 19-XIX cWW cW-W 4 D.DG4 T.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=7 strand-1 5'-CAGTAAu-3' bp-type |||||.| strand-2 3'-GTCATgA-5' helix-form BBBB.x 1 P.DC1 T.DG11 C-G WC 19-XIX cWW cW-W 2 P.DA2 T.DT10 A-T WC 20-XX cWW cW-W 3 P.DG3 T.DC9 G-C WC 19-XIX cWW cW-W 4 P.DT4 T.DA8 T-A WC 20-XX cWW cW-W 5 P.DA5 T.DT7 A-T WC 20-XX cWW cW-W 6 P.DA6 T.8OG6 A+g -- 09-IX cWH cW+M 7 A.DUP601 T.DA5 u-A WC 20-XX cWW cW-W **************************************************************************** List of 2 stems Note: A stem is defined as a helix consisting strictly of canonical WC/wobble pairs with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=4 strand-1 5'-GCCG-3' bp-type |||| strand-2 3'-CGGC-5' helix-form .BB 1 D.DG1 T.DC4 G-C WC 19-XIX cWW cW-W 2 D.DC2 T.DG3 C-G WC 19-XIX cWW cW-W 3 D.DC3 T.DG2 C-G WC 19-XIX cWW cW-W 4 D.DG4 T.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=5 strand-1 5'-CAGTA-3' bp-type ||||| strand-2 3'-GTCAT-5' helix-form BBBB 1 P.DC1 T.DG11 C-G WC 19-XIX cWW cW-W 2 P.DA2 T.DT10 A-T WC 20-XX cWW cW-W 3 P.DG3 T.DC9 G-C WC 19-XIX cWW cW-W 4 P.DT4 T.DA8 T-A WC 20-XX cWW cW-W 5 P.DA5 T.DT7 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#2] -1 T.DA5 A.DUP601 A-u WC 20-XX cWW cW-W **************************************************************************** List of 3 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 WC A.TRP274,T.DC4 2 nts=3 AAu P.DA5,P.DA6,A.DUP601 3 nts=3 AgT T.DA5,T.8OG6,T.DT7 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 A P.DA6 2 nts=1 g T.8OG6 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DC4 T.DA5 angle=131 distance=16.3 ratio=0.91 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CA T.DC4,T.DA5 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5iim nts=22 [whole] GCCG&CAGTAA&CGGCAgTACTG&u [[[[&(((((.&]]]]..)))))&. >5iim-D #1 nts=4 3.96(0.18) [chain] DNA GCCG [[[[ >5iim-P #2 nts=6 3.71(0.20) [chain] DNA CAGTAA (((((. >5iim-T #3 nts=11 3.18(1.11) [chain] DNA CGGCAgTACTG ]]]]..))))) **************************************************************************** Summary of structural features of 22 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 G [ D.DG1 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 2 C [ D.DC2 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 3 C [ D.DC3 0.005 pseudoknotted,anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 4 G [ D.DG4 0.006 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 5 C ( P.DC1 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 6 A ( P.DA2 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 G ( P.DG3 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ( P.DT4 0.007 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 9 A ( P.DA5 0.010 anti,BI,canonical,non-pair-contact,helix,stem-end,phosphate 10 A . P.DA6 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 11 C ] T.DC1 0.006 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 12 G ] T.DG2 0.007 pseudoknotted,anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 13 G ] T.DG3 0.006 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 C ] T.DC4 0.005 pseudoknotted,anti,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 15 A . T.DA5 0.013 ~C2'-endo,BI,isolated-canonical,non-pair-contact,helix-end,phosphate,splayed-apart 16 g . T.8OG6 0.151 modified,syn,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 17 T ) T.DT7 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end 18 A ) T.DA8 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 C ) T.DC9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 T ) T.DT10 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 21 G ) T.DG11 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 22 u . A.DUP601 0.041 modified,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end **************************************************************************** List of 13 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks 10 dssr-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia