**************************************************************************** File name: 4j9m.pdb no. of DNA/RNA chains: 2 [P=9,T=10] no. of nucleotides: 20 no. of atoms: 3961 no. of waters: 188 no. of metals: 3 [Na=1,Mg=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 XG4-g 1 A.XG4/504 **************************************************************************** List of 9 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DT4 A.XG4/504 T-g Wobble 28-XXVIII cWW cW-W 2 T.DT5 P.DA9 T-A WC 20-XX cWW cW-W 3 T.DA6 P.DT8 A-T WC 20-XX cWW cW-W 4 T.DT7 P.DA7 T-A WC 20-XX cWW cW-W 5 T.DG8 P.DC6 G-C WC 19-XIX cWW cW-W 6 T.DA9 P.DT5 A-T WC 20-XX cWW cW-W 7 T.DC10 P.DG4 C-G WC 19-XIX cWW cW-W 8 T.DG11 P.DC3 G-C WC 19-XIX cWW cW-W 9 T.DT12 P.DA2 T-A WC 20-XX 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=9 strand-1 5'-TTATGACGT-3' bp-type ||||||||| strand-2 3'-gATACTGCA-5' helix-form x.BBBBBB 1 T.DT4 A.XG4/504 T-g Wobble 28-XXVIII cWW cW-W 2 T.DT5 P.DA9 T-A WC 20-XX cWW cW-W 3 T.DA6 P.DT8 A-T WC 20-XX cWW cW-W 4 T.DT7 P.DA7 T-A WC 20-XX cWW cW-W 5 T.DG8 P.DC6 G-C WC 19-XIX cWW cW-W 6 T.DA9 P.DT5 A-T WC 20-XX cWW cW-W 7 T.DC10 P.DG4 C-G WC 19-XIX cWW cW-W 8 T.DG11 P.DC3 G-C WC 19-XIX cWW cW-W 9 T.DT12 P.DA2 T-A WC 20-XX 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=8 strand-1 5'-TATGACGT-3' bp-type |||||||| strand-2 3'-ATACTGCA-5' helix-form .BBBBBB 1 T.DT5 P.DA9 T-A WC 20-XX cWW cW-W 2 T.DA6 P.DT8 A-T WC 20-XX cWW cW-W 3 T.DT7 P.DA7 T-A WC 20-XX cWW cW-W 4 T.DG8 P.DC6 G-C WC 19-XIX cWW cW-W 5 T.DA9 P.DT5 A-T WC 20-XX cWW cW-W 6 T.DC10 P.DG4 C-G WC 19-XIX cWW cW-W 7 T.DG11 P.DC3 G-C WC 19-XIX cWW cW-W 8 T.DT12 P.DA2 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. -------------------------------------------------------------------- [#1] -1 T.DT4 A.XG4/504 T-g Wobble 28-XXVIII 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.TRP42,T.DC3 2 nts=2 RA A.ARG61,P.DA9 3 nts=2 TT T.DT4,T.DT5 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 g A.XG4/504 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 C T.DC3 2 nts=1 T P.DT1 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DC3 T.DT4 angle=137 distance=17.6 ratio=0.93 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CT T.DC3,T.DT4 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4j9m nts=20 [whole] CTTATGACGT&TACGTCATA&g ..((((((((&.))))))))&. >4j9m-T #1 nts=10 3.28(0.34) [chain] DNA CTTATGACGT ..(((((((( >4j9m-P #2 nts=9 3.77(0.23) [chain] DNA TACGTCATA .)))))))) **************************************************************************** Summary of structural features of 20 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 . T.DC3 0.002 anti,~C2'-endo,ss-non-loop,splayed-apart 2 T . T.DT4 0.002 anti,~C2'-endo,BI,isolated-canonical,non-pair-contact,helix-end,phosphate,splayed-apart 3 T ( T.DT5 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 4 A ( T.DA6 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( T.DT7 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 G ( T.DG8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 A ( T.DA9 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 C ( T.DC10 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 G ( T.DG11 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 T ( T.DT12 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 11 T . P.DT1 --- non-stack,ss-non-loop 12 A ) P.DA2 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 13 C ) P.DC3 0.007 anti,BI,canonical,non-pair-contact,helix,stem 14 G ) P.DG4 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 15 T ) P.DT5 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 C ) P.DC6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 17 A ) P.DA7 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 T ) P.DT8 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 19 A ) P.DA9 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end 20 g . A.XG4/504 0.073 modified,anti,~C3'-endo,non-stack,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