**************************************************************************** File name: 9jf9.pdb no. of DNA/RNA chains: 2 [C=24,D=24] no. of nucleotides: 48 no. of atoms: 14018 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 6 types of 32 modified nucleotides nt count list 1 85Y-t 6 C.85Y10,C.85Y16,C.85Y20,D.85Y10,D.85Y16,D.85Y20 2 AF2-a 6 C.AF2/2,C.AF2/12,C.AF2/19,D.AF2/2,D.AF2/12,D.AF2/19 3 CFZ-c 6 C.CFZ6,C.CFZ8,C.CFZ22,D.CFZ6,D.CFZ8,D.CFZ22 4 DUZ-t 8 C.DUZ3,C.DUZ4,C.DUZ14,C.DUZ24,D.DUZ3,D.DUZ4,D.DUZ14,D.DUZ24 5 OMC-c 2 C.OMC21,D.OMC21 6 OMG-g 4 C.OMG11,C.OMG13,D.OMG11,D.OMG13 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DA5 C.DUZ24 A-t WC 20-XX cWW cW-W 2 C.CFZ6 C.DG23 c-G WC 19-XIX cWW cW-W 3 C.DG7 C.CFZ22 G-c WC 19-XIX cWW cW-W 4 C.OMG11 C.DG18 g+G -- -- tSS tm+m 5 C.OMG11 C.OMC21 g-c WC 19-XIX cWW cW-W 6 C.DUZ14 C.DA17 t+A -- -- cWH cW+M 7 D.DA5 D.DG23 A-G Imino 08-VIII cWW cW-W 8 D.DA5 D.DUZ24 A-t WC 20-XX cWW cW-W 9 D.CFZ6 D.DG23 c-G WC 19-XIX cWW cW-W 10 D.DG7 D.CFZ22 G-c WC 19-XIX cWW cW-W 11 D.OMG11 D.DG18 g+G -- -- tSS tm+m 12 D.OMG11 D.OMC21 g-c ~Wobble -- cWW cW-W **************************************************************************** List of 1 multiplet 1 nts=3 gGc C.OMG11,C.DG18,C.OMC21 **************************************************************************** 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=3 strand-1 5'-AcG-3' bp-type ||| strand-2 3'-tGc-5' helix-form .. 1 C.DA5 C.DUZ24 A-t WC 20-XX cWW cW-W 2 C.CFZ6 C.DG23 c-G WC 19-XIX cWW cW-W 3 C.DG7 C.CFZ22 G-c WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=3 strand-1 5'-AcG-3' bp-type ||| strand-2 3'-tGc-5' helix-form .. 1 D.DA5 D.DUZ24 A-t WC 20-XX cWW cW-W 2 D.CFZ6 D.DG23 c-G WC 19-XIX cWW cW-W 3 D.DG7 D.CFZ22 G-c WC 19-XIX 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=3 strand-1 5'-AcG-3' bp-type ||| strand-2 3'-tGc-5' helix-form .. 1 C.DA5 C.DUZ24 A-t WC 20-XX cWW cW-W 2 C.CFZ6 C.DG23 c-G WC 19-XIX cWW cW-W 3 C.DG7 C.CFZ22 G-c WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=3 strand-1 5'-AcG-3' bp-type ||| strand-2 3'-tGc-5' helix-form .. 1 D.DA5 D.DUZ24 A-t WC 20-XX cWW cW-W 2 D.CFZ6 D.DG23 c-G WC 19-XIX cWW cW-W 3 D.DG7 D.CFZ22 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 C.OMG11 C.OMC21 g-c WC 19-XIX cWW cW-W **************************************************************************** List of 11 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 Yt A.TYR477,D.DUZ4 2 nts=2 FC B.PHE88,D.DC15 3 nts=2 Yt B.TYR477,C.DUZ4 4 nts=2 Ca C.DC1,C.AF2/2 5 nts=2 gt C.OMG13,C.DUZ14 6 nts=2 Ca D.DC1,D.AF2/2 7 nts=2 gt D.OMG13,D.DUZ14 8 nts=4 RaGA A.ARG554,D.AF2/12,D.DG18,D.DA17 9 nts=4 Atga C.DA9,C.85Y10,C.OMG11,C.AF2/19 10 nts=5 RAtga B.ARG65,D.DA9,D.85Y10,D.OMG11,D.AF2/19 11 nts=5 RaGAt B.ARG554,C.AF2/12,C.DG18,C.DA17,C.85Y16 **************************************************************************** Nucleotides not involved in stacking interactions nts=10 tcCtctcttc C.DUZ3,C.CFZ8,C.DC15,C.85Y20,C.OMC21,D.DUZ3,D.CFZ8,D.85Y16,D.85Y20,D.OMC21 **************************************************************************** List of 11 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate O3'@C.DG7 C.CFZ8 3.33 2 other N23@C.DUZ14 C.OMG13 3.37 3 phosphate OP1@C.DC15 C.DC15 3.13 4 other O2@C.85Y16 C.DA17 3.02 5 sugar O4'@C.AF2/19 C.OMC21 2.96 6 phosphate OP1@D.DC1 D.DC1 3.14 7 phosphate O3'@D.DG7 D.CFZ8 3.12 8 other N1@D.85Y10 D.OMG11 3.49 9 phosphate OP1@D.DC15 D.DC15 3.05 10 other O2@D.85Y16 D.DA17 2.86 11 sugar O4'@D.AF2/19 D.OMC21 3.10 **************************************************************************** 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 2 hairpin loops 1 hairpin loop: nts=11; [9]; linked by [#-1] summary: [1] 9 [C.11 C.21] 1 nts=11 gagtCtAGatc C.OMG11,C.AF2/12,C.OMG13,C.DUZ14,C.DC15,C.85Y16,C.DA17,C.DG18,C.AF2/19,C.85Y20,C.OMC21 nts=9 agtCtAGat C.AF2/12,C.OMG13,C.DUZ14,C.DC15,C.85Y16,C.DA17,C.DG18,C.AF2/19,C.85Y20 2 hairpin loop: nts=16; [14]; linked by [#2] summary: [1] 14 [D.7 D.22] 3 nts=16 GcAtgagtCtAGatcc D.DG7,D.CFZ8,D.DA9,D.85Y10,D.OMG11,D.AF2/12,D.OMG13,D.DUZ14,D.DC15,D.85Y16,D.DA17,D.DG18,D.AF2/19,D.85Y20,D.OMC21,D.CFZ22 nts=14 cAtgagtCtAGatc D.CFZ8,D.DA9,D.85Y10,D.OMG11,D.AF2/12,D.OMG13,D.DUZ14,D.DC15,D.85Y16,D.DA17,D.DG18,D.AF2/19,D.85Y20,D.OMC21 **************************************************************************** List of 1 bulge 1 bulge: nts=7; [3,0]; linked by [#1,#-1] summary: [2] 3 0 [C.7 C.22 C.11 C.21] 3 1 nts=7 GcAtgcc C.DG7,C.CFZ8,C.DA9,C.85Y10,C.OMG11,C.OMC21,C.CFZ22 nts=3 cAt C.CFZ8,C.DA9,C.85Y10 nts=0 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=4 Catt C.DC1,C.AF2/2,C.DUZ3,C.DUZ4 2 nts=4 Catt D.DC1,D.AF2/2,D.DUZ3,D.DUZ4 **************************************************************************** List of 14 splayed-apart dinucleotides 1 C.AF2/2 C.DUZ3 angle=93 distance=13.6 ratio=0.73 2 C.DUZ3 C.DUZ4 angle=96 distance=13.6 ratio=0.74 3 C.CFZ8 C.DA9 angle=118 distance=18.4 ratio=0.86 4 C.DUZ14 C.DC15 angle=124 distance=12.4 ratio=0.88 5 C.DC15 C.85Y16 angle=106 distance=17.4 ratio=0.80 6 C.AF2/19 C.85Y20 angle=157 distance=19.0 ratio=0.98 7 C.85Y20 C.OMC21 angle=113 distance=17.1 ratio=0.83 8 D.AF2/2 D.DUZ3 angle=94 distance=13.7 ratio=0.74 9 D.DUZ3 D.DUZ4 angle=92 distance=13.3 ratio=0.72 10 D.CFZ8 D.DA9 angle=125 distance=18.9 ratio=0.89 11 D.DUZ14 D.DC15 angle=107 distance=11.9 ratio=0.81 12 D.DC15 D.85Y16 angle=111 distance=17.5 ratio=0.82 13 D.AF2/19 D.85Y20 angle=159 distance=18.6 ratio=0.98 14 D.85Y20 D.OMC21 angle=106 distance=16.5 ratio=0.80 ---------------------------------------------------------------- Summary of 8 splayed-apart units 1 nts=3 att C.AF2/2,C.DUZ3,C.DUZ4 2 nts=2 cA C.CFZ8,C.DA9 3 nts=3 tCt C.DUZ14,C.DC15,C.85Y16 4 nts=3 atc C.AF2/19,C.85Y20,C.OMC21 5 nts=3 att D.AF2/2,D.DUZ3,D.DUZ4 6 nts=2 cA D.CFZ8,D.DA9 7 nts=3 tCt D.DUZ14,D.DC15,D.85Y16 8 nts=3 atc D.AF2/19,D.85Y20,D.OMC21 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9jf9 nts=48 [whole] CattAcGcAtgagtCtAGatccGt&CattAcGcAtgagtCtAGatccGt ....(((...(.........))))&....(((..............))) >9jf9-C #1 nts=24 0.10(2.67) [chain] DNA[15]/RNA[9] CattAcGcAtgagtCtAGatccGt ....(((...(.........)))) >9jf9-D #2 nts=24 0.10(2.60) [chain] DNA[15]/RNA[9] CattAcGcAtgagtCtAGatccGt ....(((..............))) **************************************************************************** Summary of structural features of 48 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 . C.DC1 0.003 ~C2'-endo,non-pair-contact,ss-non-loop 2 a . C.AF2/2 0.063 modified,anti,BII,non-pair-contact,ss-non-loop,splayed-apart 3 t . C.DUZ3 0.119 modified,~C2'-endo,non-stack,ss-non-loop,splayed-apart 4 t . C.DUZ4 0.118 modified,anti,ss-non-loop,splayed-apart 5 A ( C.DA5 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 6 c ( C.CFZ6 0.111 modified,anti,~C2'-endo,canonical,non-pair-contact,helix,stem 7 G ( C.DG7 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,bulge,cap-donor 8 c . C.CFZ8 0.112 modified,turn,BI,non-stack,bulge,cap-acceptor,splayed-apart 9 A . C.DA9 0.006 anti,~C2'-endo,BI,non-pair-contact,bulge,phosphate,splayed-apart 10 t . C.85Y10 0.156 modified,syn,~C3'-endo,BI,non-pair-contact,bulge 11 g ( C.OMG11 0.125 modified,anti,~C2'-endo,isolated-canonical,non-canonical,non-pair-contact,multiplet,hairpin-loop,bulge 12 a . C.AF2/12 0.063 modified,anti,non-pair-contact,hairpin-loop 13 g . C.OMG13 0.124 modified,turn,~C3'-endo,non-pair-contact,hairpin-loop,cap-acceptor 14 t . C.DUZ14 0.121 modified,anti,non-canonical,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 15 C . C.DC15 0.002 turn,~C2'-endo,non-stack,hairpin-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 16 t . C.85Y16 0.159 modified,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 17 A . C.DA17 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 18 G . C.DG18 0.003 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,hairpin-loop 19 a . C.AF2/19 0.063 modified,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 20 t . C.85Y20 0.159 modified,turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 21 c ) C.OMC21 0.011 modified,turn,anti,BI,non-stack,isolated-canonical,non-pair-contact,multiplet,hairpin-loop,bulge,cap-acceptor,splayed-apart 22 c ) C.CFZ22 0.110 modified,anti,BI,canonical,non-pair-contact,helix-end,stem-end,bulge 23 G ) C.DG23 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 24 t ) C.DUZ24 0.119 modified,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 25 C . D.DC1 0.003 ~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,cap-acceptor,phosphate 26 a . D.AF2/2 0.062 modified,anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 27 t . D.DUZ3 0.121 modified,~C2'-endo,non-stack,ss-non-loop,splayed-apart 28 t . D.DUZ4 0.116 modified,anti,non-pair-contact,ss-non-loop,splayed-apart 29 A ( D.DA5 0.004 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end 30 c ( D.CFZ6 0.110 modified,anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 31 G ( D.DG7 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,cap-donor 32 c . D.CFZ8 0.113 modified,turn,BI,non-stack,hairpin-loop,cap-acceptor,splayed-apart 33 A . D.DA9 0.004 anti,~C2'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 34 t . D.85Y10 0.158 modified,syn,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor 35 g . D.OMG11 0.123 modified,anti,~C2'-endo,non-canonical,non-pair-contact,hairpin-loop,cap-acceptor 36 a . D.AF2/12 0.062 modified,anti,non-pair-contact,hairpin-loop 37 g . D.OMG13 0.124 modified,turn,~C3'-endo,non-pair-contact,hairpin-loop 38 t . D.DUZ14 0.121 modified,anti,non-pair-contact,hairpin-loop,splayed-apart 39 C . D.DC15 0.003 turn,~C2'-endo,hairpin-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 40 t . D.85Y16 0.161 modified,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 41 A . D.DA17 0.004 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 42 G . D.DG18 0.003 anti,~C2'-endo,BII,non-canonical,non-pair-contact,hairpin-loop 43 a . D.AF2/19 0.063 modified,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 44 t . D.85Y20 0.159 modified,turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 45 c . D.OMC21 0.012 modified,turn,anti,BI,non-stack,non-canonical,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 46 c ) D.CFZ22 0.109 modified,anti,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 47 G ) D.DG23 0.004 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem 48 t ) D.DUZ24 0.119 modified,anti,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 17 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-bulges.pdb -- an ensemble of bulges 7 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 8 dssr-2ndstrs.ct -- secondary structure in connectivity table format 9 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 10 dssr-torsions.txt -- backbone torsion angles and suite names 11 dssr-splays.pdb -- an ensemble of splayed-apart units 12 dssr-stacks.pdb -- an ensemble of base stacks 13 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 14 dssr-rotmat.txt -- position vector and rotation matrix 15 dssr-viewV.pdb -- vertical view of the principal moment of inertia 16 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 17 dssr-viewT.pdb -- top view of the principal moment of inertia