**************************************************************************** File name: 9oau.pdb no. of DNA/RNA chains: 2 [P=13,T=18] no. of nucleotides: 31 no. of atoms: 7358 no. of waters: 440 no. of metals: 4 [Mg=4] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 FA2-a 1 P.FA2/13 2 TFT-t 1 P.TFT12 **************************************************************************** List of 13 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DT7 P.FA2/13 T-a WC 20-XX cWW cW-W 2 T.DA8 P.TFT12 A-t WC 20-XX cWW cW-W 3 T.DC9 P.DG11 C-G WC 19-XIX cWW cW-W 4 T.DG10 P.DC10 G-C WC 19-XIX cWW cW-W 5 T.DC11 P.DG9 C-G WC 19-XIX cWW cW-W 6 T.DA12 P.DT8 A-T WC 20-XX cWW cW-W 7 T.DG13 P.DC7 G-C WC 19-XIX cWW cW-W 8 T.DT14 P.DA6 T-A WC 20-XX cWW cW-W 9 T.DT15 P.DA5 T-A WC 20-XX cWW cW-W 10 T.DC16 P.DG4 C-G WC 19-XIX cWW cW-W 11 T.DG17 P.DC3 G-C WC 19-XIX cWW cW-W 12 T.DC18 P.DG2 C-G WC 19-XIX cWW cW-W 13 T.DG19 P.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 helix 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=13 strand-1 5'-TACGCAGTTCGCG-3' bp-type ||||||||||||| strand-2 3'-atGCGTCAAGCGC-5' helix-form xB..B.BBBBBB 1 T.DT7 P.FA2/13 T-a WC 20-XX cWW cW-W 2 T.DA8 P.TFT12 A-t WC 20-XX cWW cW-W 3 T.DC9 P.DG11 C-G WC 19-XIX cWW cW-W 4 T.DG10 P.DC10 G-C WC 19-XIX cWW cW-W 5 T.DC11 P.DG9 C-G WC 19-XIX cWW cW-W 6 T.DA12 P.DT8 A-T WC 20-XX cWW cW-W 7 T.DG13 P.DC7 G-C WC 19-XIX cWW cW-W 8 T.DT14 P.DA6 T-A WC 20-XX cWW cW-W 9 T.DT15 P.DA5 T-A WC 20-XX cWW cW-W 10 T.DC16 P.DG4 C-G WC 19-XIX cWW cW-W 11 T.DG17 P.DC3 G-C WC 19-XIX cWW cW-W 12 T.DC18 P.DG2 C-G WC 19-XIX cWW cW-W 13 T.DG19 P.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 stem 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=12 strand-1 5'-ACGCAGTTCGCG-3' bp-type |||||||||||| strand-2 3'-tGCGTCAAGCGC-5' helix-form B..B.BBBBBB 1 T.DA8 P.TFT12 A-t WC 20-XX cWW cW-W 2 T.DC9 P.DG11 C-G WC 19-XIX cWW cW-W 3 T.DG10 P.DC10 G-C WC 19-XIX cWW cW-W 4 T.DC11 P.DG9 C-G WC 19-XIX cWW cW-W 5 T.DA12 P.DT8 A-T WC 20-XX cWW cW-W 6 T.DG13 P.DC7 G-C WC 19-XIX cWW cW-W 7 T.DT14 P.DA6 T-A WC 20-XX cWW cW-W 8 T.DT15 P.DA5 T-A WC 20-XX cWW cW-W 9 T.DC16 P.DG4 C-G WC 19-XIX cWW cW-W 10 T.DG17 P.DC3 G-C WC 19-XIX cWW cW-W 11 T.DC18 P.DG2 C-G WC 19-XIX cWW cW-W 12 T.DG19 P.DC1 G-C WC 19-XIX 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. -------------------------------------------------------------------- [#1] -1 T.DT7 P.FA2/13 T-a WC 20-XX cWW cW-W **************************************************************************** List of 4 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 TA T.DT7,T.DA8 2 nts=2 ta P.TFT12,P.FA2/13 3 nts=3 RCG A.ARG247,T.DC5,T.DG6 4 nts=4 RAAA A.ARG502,T.DA4,T.DA3,T.DA2 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C P.DC1 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@T.DC5 T.DG6 2.88 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=5 AAACG T.DA2,T.DA3,T.DA4,T.DC5,T.DG6 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DA4 T.DC5 angle=173 distance=19.7 ratio=1.00 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 AC T.DA4,T.DC5 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9oau nts=31 [whole] AAACGTACGCAGTTCGCG&CGCGAACTGCGt&a .....(((((((((((((&))))))))))))&) >9oau-T #1 nts=18 3.00(1.01) [chain] DNA AAACGTACGCAGTTCGCG .....((((((((((((( >9oau-P #2 nts=13 3.25(0.52) [chain] DNA[12]/1* CGCGAACTGCGt&a ))))))))))))&) **************************************************************************** Summary of structural features of 31 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 A . T.DA2 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 A . T.DA3 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 3 A . T.DA4 0.003 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 4 C . T.DC5 0.003 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,phosphate,splayed-apart 5 G . T.DG6 0.005 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor 6 T ( T.DT7 0.003 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end 7 A ( T.DA8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 8 C ( T.DC9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 G ( T.DG10 0.003 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 10 C ( T.DC11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 A ( T.DA12 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 12 G ( T.DG13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 T ( T.DT14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 T ( T.DT15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 15 C ( T.DC16 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 16 G ( T.DG17 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ( T.DC18 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 G ( T.DG19 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 19 C ) P.DC1 0.003 anti,~C2'-endo,non-stack,canonical,helix-end,stem-end 20 G ) P.DG2 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ) P.DC3 0.002 anti,BI,canonical,non-pair-contact,helix,stem 22 G ) P.DG4 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 A ) P.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 A ) P.DA6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 25 C ) P.DC7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 T ) P.DT8 0.002 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 27 G ) P.DG9 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 28 C ) P.DC10 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 G ) P.DG11 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 30 t ) P.TFT12 0.060 modified,break,canonical,non-pair-contact,helix,stem-end,phosphate 31 a ) P.FA2/13 0.084 modified,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,phosphate **************************************************************************** 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-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-atom2bases.pdb -- an ensemble of atom-base stacking interactions 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