**************************************************************************** File name: 6cr5.pdb no. of DNA/RNA chains: 3 [D=5,P=10,T=16] no. of nucleotides: 32 no. of atoms: 3508 no. of waters: 231 no. of metals: 4 [Na=3,Mg=1] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 DOC-c 1 P.DOC10 2 FCJ-a 1 A.FCJ401 **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W 6 T.DT6 A.FCJ401 T-a WC 20-XX cWW cW-W 7 T.DG7 P.DOC10 G-c WC 19-XIX cWW cW-W 8 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 9 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 10 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 11 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 12 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 13 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 14 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 15 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 16 T.DC16 P.DG1 C-G WC 19-XIX 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=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form B.B. 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=11 strand-1 5'-TGCGCATCAGC-3' bp-type ||||||||||| strand-2 3'-acGCGTAGTCG-5' helix-form xB.BBBBBBB 1 T.DT6 A.FCJ401 T-a WC 20-XX cWW cW-W 2 T.DG7 P.DOC10 G-c WC 19-XIX cWW cW-W 3 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 4 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 5 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 6 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 7 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 8 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 9 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 10 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 11 T.DC16 P.DG1 C-G 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=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form B.B. 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=10 strand-1 5'-GCGCATCAGC-3' bp-type |||||||||| strand-2 3'-cGCGTAGTCG-5' helix-form B.BBBBBBB 1 T.DG7 P.DOC10 G-c WC 19-XIX cWW cW-W 2 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 3 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 4 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 5 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 6 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 7 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 8 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 9 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 10 T.DC16 P.DG1 C-G 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. -------------------------------------------------------------------- [#2] -1 T.DT6 A.FCJ401 T-a WC 20-XX 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 CH T.DC5,A.HIS34 2 nts=2 TG T.DT6,T.DG7 3 nts=2 ca P.DOC10,A.FCJ401 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DC5 T.DT6 angle=131 distance=16.5 ratio=0.91 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CT T.DC5,T.DT6 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6cr5 nts=32 [whole] CCGACTGCGCATCAGC&GCTGATGCGc>CGG&a (((((.((((((((((&))))))))))&)))))&. >6cr5-T #1 nts=16 2.77(1.27) [chain] DNA CCGACTGCGCATCAGC (((((.(((((((((( >6cr5-P #2 nts=10 3.24(0.30) [chain] DNA GCTGATGCGc )))))))))) >6cr5-D #3 nts=5 3.66(0.09) [chain] DNA GTCGG ))))) **************************************************************************** Summary of structural features of 32 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.DC1 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( T.DC2 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 3 G ( T.DG3 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 4 A ( T.DA4 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( T.DC5 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 6 T . T.DT6 0.011 anti,~C2'-endo,BI,isolated-canonical,non-pair-contact,helix-end,phosphate,splayed-apart 7 G ( T.DG7 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 8 C ( T.DC8 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 9 G ( T.DG9 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 C ( T.DC10 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 A ( T.DA11 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 T ( T.DT12 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( T.DC13 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 A ( T.DA14 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ( T.DG15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( T.DC16 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 17 G ) P.DG1 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 18 C ) P.DC2 0.004 anti,BI,canonical,non-pair-contact,helix,stem 19 T ) P.DT3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 G ) P.DG4 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 21 A ) P.DA5 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ) P.DT6 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 G ) P.DG7 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 C ) P.DC8 0.006 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) P.DG9 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 c ) P.DOC10 0.004 modified,anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,phosphate 27 G ) D.DG1 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 28 T ) D.DT2 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 C ) D.DC3 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 30 G ) D.DG4 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 G ) D.DG5 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 32 a . A.FCJ401 0.032 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