**************************************************************************** File name: 6xdw.pdb no. of DNA/RNA chains: 4 [A=11,B=10,C=5,D=16] no. of nucleotides: 42 no. of atoms: 856 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 20 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG3 D.DC16 G-C WC 19-XIX cWW cW-W 2 A.DC4 D.DG15 C-G WC 19-XIX cWW cW-W 3 A.DA5 D.DT14 A-T WC 20-XX cWW cW-W 4 A.DG6 D.DC13 G-C WC 19-XIX cWW cW-W 5 A.DA7 D.DT12 A-T WC 20-XX cWW cW-W 6 A.DC8 D.DG11 C-G WC 19-XIX cWW cW-W 7 A.DC9 D.DG10 C-G WC 19-XIX cWW cW-W 8 A.DC10 C.DG2 C-G WC 19-XIX cWW cW-W 9 A.DG11 C.DC1 G-C WC 19-XIX cWW cW-W 10 B.DA12 C.DT5 A-T WC 20-XX cWW cW-W 11 B.DC13 C.DC3 C-C -- -- cWW cW-W 12 B.DC13 C.DG4 C-G WC 19-XIX cWW cW-W 13 B.DG14 C.DC3 G-C WC 19-XIX cWW cW-W 14 B.DG15 D.DC9 G-C WC 19-XIX cWW cW-W 15 B.DC16 D.DG8 C-G WC 19-XIX cWW cW-W 16 B.DA17 D.DT7 A-T WC 20-XX cWW cW-W 17 B.DC18 D.DG6 C-G WC 19-XIX cWW cW-W 18 B.DT19 D.DA5 T-A WC 20-XX cWW cW-W 19 B.DC20 D.DG4 C-G WC 19-XIX cWW cW-W 20 B.DA21 D.DT3 A-T 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[2] bps=9 strand-1 5'-GCAGACCCG-3' bp-type ||||||||| strand-2 3'-CGTCTGGGC-5' helix-form .BBB..xB 1 A.DG3 D.DC16 G-C WC 19-XIX cWW cW-W 2 A.DC4 D.DG15 C-G WC 19-XIX cWW cW-W 3 A.DA5 D.DT14 A-T WC 20-XX cWW cW-W 4 A.DG6 D.DC13 G-C WC 19-XIX cWW cW-W 5 A.DA7 D.DT12 A-T WC 20-XX cWW cW-W 6 A.DC8 D.DG11 C-G WC 19-XIX cWW cW-W 7 A.DC9 D.DG10 C-G WC 19-XIX cWW cW-W 8 A.DC10 C.DG2 C-G WC 19-XIX cWW cW-W 9 A.DG11 C.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[2] bps=10 strand-1 5'-ACGGCACTCA-3' bp-type |||||||||| strand-2 3'-TGCCGTGAGT-5' helix-form ..xBB..B. 1 B.DA12 C.DT5 A-T WC 20-XX cWW cW-W 2 B.DC13 C.DG4 C-G WC 19-XIX cWW cW-W 3 B.DG14 C.DC3 G-C WC 19-XIX cWW cW-W 4 B.DG15 D.DC9 G-C WC 19-XIX cWW cW-W 5 B.DC16 D.DG8 C-G WC 19-XIX cWW cW-W 6 B.DA17 D.DT7 A-T WC 20-XX cWW cW-W 7 B.DC18 D.DG6 C-G WC 19-XIX cWW cW-W 8 B.DT19 D.DA5 T-A WC 20-XX cWW cW-W 9 B.DC20 D.DG4 C-G WC 19-XIX cWW cW-W 10 B.DA21 D.DT3 A-T WC 20-XX cWW cW-W **************************************************************************** List of 4 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=7 strand-1 5'-GCAGACC-3' bp-type ||||||| strand-2 3'-CGTCTGG-5' helix-form .BBB.. 1 A.DG3 D.DC16 G-C WC 19-XIX cWW cW-W 2 A.DC4 D.DG15 C-G WC 19-XIX cWW cW-W 3 A.DA5 D.DT14 A-T WC 20-XX cWW cW-W 4 A.DG6 D.DC13 G-C WC 19-XIX cWW cW-W 5 A.DA7 D.DT12 A-T WC 20-XX cWW cW-W 6 A.DC8 D.DG11 C-G WC 19-XIX cWW cW-W 7 A.DC9 D.DG10 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form B 1 A.DC10 C.DG2 C-G WC 19-XIX cWW cW-W 2 A.DG11 C.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=3 strand-1 5'-ACG-3' bp-type ||| strand-2 3'-TGC-5' helix-form .. 1 B.DA12 C.DT5 A-T WC 20-XX cWW cW-W 2 B.DC13 C.DG4 C-G WC 19-XIX cWW cW-W 3 B.DG14 C.DC3 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#2] bps=7 strand-1 5'-GCACTCA-3' bp-type ||||||| strand-2 3'-CGTGAGT-5' helix-form BB..B. 1 B.DG15 D.DC9 G-C WC 19-XIX cWW cW-W 2 B.DC16 D.DG8 C-G WC 19-XIX cWW cW-W 3 B.DA17 D.DT7 A-T WC 20-XX cWW cW-W 4 B.DC18 D.DG6 C-G WC 19-XIX cWW cW-W 5 B.DT19 D.DA5 T-A WC 20-XX cWW cW-W 6 B.DC20 D.DG4 C-G WC 19-XIX cWW cW-W 7 B.DA21 D.DT3 A-T WC 20-XX cWW cW-W **************************************************************************** List of 2 coaxial stacks 1 Helix#1 contains 2 stems: [#1,#2] 2 Helix#2 contains 2 stems: [#3,#4] **************************************************************************** List of 6 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 CC A.DC9,A.DC10 2 nts=2 GG B.DG14,B.DG15 3 nts=2 GG C.DG2,D.DG10 4 nts=2 CC C.DC3,D.DC9 5 nts=3 GAG A.DG1,A.DA2,A.DG3 6 nts=3 TCT D.DT1,D.DC2,D.DT3 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 1 junction 1 4-way junction: nts=8; [0,0,0,0]; linked by [#1,#2,#3,#4] summary: [4] 0 0 0 0 [A.9 D.10 A.10 C.2 C.3 B.14 B.15 D.9] 7 2 3 7 nts=8 CCGCGGCG A.DC9,A.DC10,C.DG2,C.DC3,B.DG14,B.DG15,D.DC9,D.DG10 nts=0 nts=0 nts=0 nts=0 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 GA A.DG1,A.DA2 2 nts=2 TC D.DT1,D.DC2 **************************************************************************** List of 2 splayed-apart dinucleotides 1 C.DG2 C.DC3 angle=127 distance=17.4 ratio=0.90 2 D.DC9 D.DG10 angle=124 distance=17.4 ratio=0.89 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 GC C.DG2,C.DC3 2 nts=2 CG D.DC9,D.DG10 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *2-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 >6xdw nts=42 [whole] GAGCAGACCCG&ACGGCACTCA&CGCGT&TCTGAGTGCGGTCTGC ..((((((({{&[[[(((((((&}}]]]&..)))))))))))))) >6xdw-A #1 nts=11 3.33(0.46) [chain] DNA GAGCAGACCCG ..((((((({{ >6xdw-B #2 nts=10 3.14(0.29) [chain] DNA ACGGCACTCA [[[((((((( >6xdw-C #3 nts=5 3.18(0.63) [chain] DNA CGCGT }}]]] >6xdw-D #4 nts=16 0.17(1.62) [chain] DNA TCTGAGTGCGGTCTGC ..)))))))))))))) **************************************************************************** Summary of structural features of 42 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 . A.DG1 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop 2 A . A.DA2 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 3 G ( A.DG3 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 4 C ( A.DC4 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 A ( A.DA5 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 6 G ( A.DG6 0.011 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 A ( A.DA7 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 C ( A.DC8 0.008 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 C ( A.DC9 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 10 C { A.DC10 0.007 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 11 G { A.DG11 0.011 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 12 A [ B.DA12 0.006 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 13 C [ B.DC13 0.013 pseudoknotted,anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 14 G [ B.DG14 0.019 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 15 G ( B.DG15 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 16 C ( B.DC16 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 A ( B.DA17 0.011 BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 C ( B.DC18 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 19 T ( B.DT19 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 20 C ( B.DC20 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 A ( B.DA21 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 22 C } C.DC1 0.009 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 23 G } C.DG2 0.012 pseudoknotted,anti,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 24 C ] C.DC3 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 25 G ] C.DG4 0.015 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 T ] C.DT5 0.008 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 27 T . D.DT1 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 28 C . D.DC2 0.006 anti,BI,non-pair-contact,ss-non-loop 29 T ) D.DT3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 30 G ) D.DG4 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 A ) D.DA5 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 G ) D.DG6 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 33 T ) D.DT7 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 G ) D.DG8 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 C ) D.DC9 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 36 G ) D.DG10 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 37 G ) D.DG11 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 38 T ) D.DT12 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 39 C ) D.DC13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 T ) D.DT14 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 41 G ) D.DG15 0.013 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 42 C ) D.DC16 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 14 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-junctions.pdb -- an ensemble of junctions (multi-branch) 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 9 dssr-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-rotmat.txt -- position vector and rotation matrix 12 dssr-viewV.pdb -- vertical view of the principal moment of inertia 13 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 14 dssr-viewT.pdb -- top view of the principal moment of inertia