**************************************************************************** File name: 6p71.pdb no. of DNA/RNA chains: 3 [G=15,H=16,I=4] no. of nucleotides: 36 no. of atoms: 28417 no. of waters: 0 no. of metals: 4 [Mg=2,Zn=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 UTP-u 1 D.UTP2005 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 G.DT7 H.DA21 T-A WC 20-XX cWW cW-W 2 G.DC8 H.DG20 C-G WC 19-XIX cWW cW-W 3 G.DC9 H.DG19 C-G WC 19-XIX cWW cW-W 4 G.DC10 H.DG18 C-G WC 19-XIX cWW cW-W 5 G.DG11 H.DC17 G-C WC 19-XIX cWW cW-W 6 G.DG12 H.DC16 G-C WC 19-XIX cWW cW-W 7 G.DC13 H.DG15 C-G WC 19-XIX cWW cW-W 8 G.DA14 D.UTP2005 A-u WC 20-XX cWW cW-W 9 G.DA15 I.U3 A-U WC 20-XX cWW cW-W 10 G.DA16 I.U2 A-U WC 20-XX cWW cW-W 11 G.DT17 I.A1 T-A WC 20-XX cWW cW-W 12 G.DT18 I.A0 T-A 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=7 strand-1 5'-TCCCGGC-3' bp-type ||||||| strand-2 3'-AGGGCCG-5' helix-form BBB... 1 G.DT7 H.DA21 T-A WC 20-XX cWW cW-W 2 G.DC8 H.DG20 C-G WC 19-XIX cWW cW-W 3 G.DC9 H.DG19 C-G WC 19-XIX cWW cW-W 4 G.DC10 H.DG18 C-G WC 19-XIX cWW cW-W 5 G.DG11 H.DC17 G-C WC 19-XIX cWW cW-W 6 G.DG12 H.DC16 G-C WC 19-XIX cWW cW-W 7 G.DC13 H.DG15 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=5 strand-1 5'-AAATT-3' bp-type ||||| strand-2 3'-uUUAA-5' helix-form xA.. 1 G.DA14 D.UTP2005 A-u WC 20-XX cWW cW-W 2 G.DA15 I.U3 A-U WC 20-XX cWW cW-W 3 G.DA16 I.U2 A-U WC 20-XX cWW cW-W 4 G.DT17 I.A1 T-A WC 20-XX cWW cW-W 5 G.DT18 I.A0 T-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=7 strand-1 5'-TCCCGGC-3' bp-type ||||||| strand-2 3'-AGGGCCG-5' helix-form BBB... 1 G.DT7 H.DA21 T-A WC 20-XX cWW cW-W 2 G.DC8 H.DG20 C-G WC 19-XIX cWW cW-W 3 G.DC9 H.DG19 C-G WC 19-XIX cWW cW-W 4 G.DC10 H.DG18 C-G WC 19-XIX cWW cW-W 5 G.DG11 H.DC17 G-C WC 19-XIX cWW cW-W 6 G.DG12 H.DC16 G-C WC 19-XIX cWW cW-W 7 G.DC13 H.DG15 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=4 strand-1 5'-AATT-3' bp-type |||| strand-2 3'-UUAA-5' helix-form A.. 1 G.DA15 I.U3 A-U WC 20-XX cWW cW-W 2 G.DA16 I.U2 A-U WC 20-XX cWW cW-W 3 G.DT17 I.A1 T-A WC 20-XX cWW cW-W 4 G.DT18 I.A0 T-A 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 G.DA14 D.UTP2005 A-u WC 20-XX cWW cW-W **************************************************************************** List of 7 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 CT G.DC6,G.DT7 2 nts=2 AA G.DA14,G.DA15 3 nts=2 GA H.DG8,H.DA9 4 nts=2 Uu I.U3,D.UTP2005 5 nts=3 RAY F.ARG231,H.DA2,F.TYR238 6 nts=3 TGA G.DT20,G.DG19,I.A0 7 nts=3 TAA H.DT3,H.DA4,H.DA5 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 TT H.DT1,H.DT6 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=1 C G.DC6 2 nts=2 GT G.DG19,G.DT20 3 nts=9 TATAATCGA H.DT1,H.DA2,H.DT3,H.DA4,H.DA5,H.DT6,H.DC7,H.DG8,H.DA9 **************************************************************************** List of 4 splayed-apart dinucleotides 1 G.DC13 G.DA14 angle=133 distance=17.8 ratio=0.92 2 H.DA2 H.DT3 angle=140 distance=18.9 ratio=0.94 3 H.DA5 H.DT6 angle=87 distance=13.6 ratio=0.69 4 H.DT6 H.DC7 angle=107 distance=16.4 ratio=0.80 ---------------------------------------------------------------- Summary of 3 splayed-apart units 1 nts=2 CA G.DC13,G.DA14 2 nts=2 AT H.DA2,H.DT3 3 nts=3 ATC H.DA5,H.DT6,H.DC7 **************************************************************************** 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 >6p71 nts=36 [whole] CTCCCGGCAAATTGT&TATAATCGA&GCCGGGA&AAUU&u .(((((((.[[[[..&.........&)))))))&]]]]&. >6p71-G #1 nts=15 3.41(1.04) [chain] DNA CTCCCGGCAAATTGT .(((((((.[[[[.. >6p71-H #2 nts=16 2.24(2.35) [chain] DNA* TATAATCGA&GCCGGGA .........&))))))) >6p71-I #3 nts=4 1.60(0.13) [chain] RNA AAUU ]]]] **************************************************************************** Summary of structural features of 36 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 C . G.DC6 0.010 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 T ( G.DT7 0.005 ~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 3 C ( G.DC8 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 4 C ( G.DC9 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( G.DC10 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 G ( G.DG11 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 G ( G.DG12 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 C ( G.DC13 0.007 anti,~C3'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 9 A . G.DA14 0.009 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,phosphate,splayed-apart 10 A [ G.DA15 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 11 A [ G.DA16 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 T [ G.DT17 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 T [ G.DT18 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 14 G . G.DG19 0.019 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 15 T . G.DT20 0.001 syn,~C2'-endo,non-pair-contact,ss-non-loop 16 T . H.DT1 0.011 syn,~C3'-endo,BI,non-stack,ss-non-loop 17 A . H.DA2 0.009 anti,~C2'-endo,BII,ss-non-loop,splayed-apart 18 T . H.DT3 0.010 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 19 A . H.DA4 0.012 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 20 A . H.DA5 0.012 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 21 T . H.DT6 0.005 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 22 C . H.DC7 0.010 anti,~C2'-endo,ss-non-loop,splayed-apart 23 G . H.DG8 0.008 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 24 A . H.DA9 0.009 break,anti,~C2'-endo,non-pair-contact,ss-non-loop 25 G ) H.DG15 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 26 C ) H.DC16 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 C ) H.DC17 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 G ) H.DG18 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 G ) H.DG19 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 30 G ) H.DG20 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 31 A ) H.DA21 0.011 anti,canonical,non-pair-contact,helix-end,stem-end 32 A ] I.A0 0.008 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 33 A ] I.A1 0.006 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 34 U ] I.U2 0.011 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 35 U ] I.U3 0.014 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,phosphate 36 u . D.UTP2005 0.047 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