3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Vandana on May 24, 2012, 01:58:05 am

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Title: This structure has broken O3' to P[i+1] linkages
Post by: Vandana on May 24, 2012, 01:58:05 am

Hello dr Lu and other users,
I am new to 3DNA. I ran a pdb file with find_pair followed by analyze. I got this msg "This structure has broken O3' to P[i+1] linkages.". could any one help me in understanding what this means?? Also i need to know the major groove and minor groove which application do i run for the same. I have attached the pdb file i have used.

Regards
Vandana.R

Title: Re: This structure has broken O3' to P[i+1] linkages
Post by: xiangjun on May 24, 2012, 02:17:04 pm

Thanks for using 3DNA. Regarding 1le5, if you display 1le5.pdb (downloaded from PDB) in Jmol/PyMOL/RasMol, you will immediately notice that the structure in its asymmetric unit contains two copies of DNA duplexes (http://ndbserver.rutgers.edu/atlas/xray/structures/P/pd0307/PD0307-asym.html). The two 'fragments' are not covalently connected, thus the message "This structure has broken O3' to P[i+1] linkages." -- it is for information only, not an error.

For the benefit of other viewers, here is what it looks like:

find_pair 1le5.pdb 1le5.inp
File '1le5.inp' has the following content:
1le5.pdb
1le5.out
    2         # duplex
   22         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    2   24  0 #    1 | ....>C:...2_:[GUA]G-----C[CYT]:..24_:D<....  0.61  0.60 14.96  9.14 -2.43
    3   23  0 #    2 | ....>C:...3_:[GUA]G-----C[CYT]:..23_:D<....  1.51  1.46 20.49  8.77  0.45
    4   22  0 #    3 | ....>C:...4_:[GUA]G-----C[CYT]:..22_:D<....  0.22  0.16 15.16  9.16 -3.69
    5   21  0 #    4 | ....>C:...5_:[ADE]A-----T[THY]:..21_:D<....  0.62  0.47 31.07  9.04 -1.89
    6   20  0 #    5 | ....>C:...6_:[ADE]A-----T[THY]:..20_:D<....  0.29  0.26  5.82  8.99 -3.91
    7   19  0 #    6 | ....>C:...7_:[ADE]A-----T[THY]:..19_:D<....  0.33  0.28 13.21  8.86 -3.45
    8   18  0 #    7 | ....>C:...8_:[THY]T-----A[ADE]:..18_:D<....  0.38  0.31 21.55  8.63 -2.92
    9   17  0 #    8 | ....>C:...9_:[THY]T-----A[ADE]:..17_:D<....  1.06  1.02 10.85  8.99 -1.37
   10   16  0 #    9 | ....>C:..10_:[CYT]C-----G[GUA]:..16_:D<....  1.03  1.00  4.76  9.04 -1.73
   11   15  0 #   10 | ....>C:..11_:[CYT]C-----G[GUA]:..15_:D<....  0.56  0.51 11.05  9.05 -2.87
   12   14  9 #   11 x ....>C:..12_:[THY]T-----A[ADE]:..14_:D<....  0.55  0.50 30.25  8.91 -1.94
   26   48  0 #   12 | ....>G:...2_:[GUA]G-----C[CYT]:..24_:H<....  0.88  0.72  5.00  8.59 -2.43
   27   47  0 #   13 | ....>G:...3_:[GUA]G-----C[CYT]:..23_:H<....  1.08  0.96 14.49  8.78 -1.27
   28   46  0 #   14 | ....>G:...4_:[GUA]G-----C[CYT]:..22_:H<....  0.40  0.24 12.49  8.79 -3.50
   29   45  0 #   15 | ....>G:...5_:[ADE]A-----T[THY]:..21_:H<....  0.41  0.30 13.27  8.63 -3.33
   30   44  0 #   16 | ....>G:...6_:[ADE]A-----T[THY]:..20_:H<....  0.95  0.80 21.23  8.37 -1.38
   31   43  0 #   17 | ....>G:...7_:[ADE]A-----T[THY]:..19_:H<....  0.86  0.81 19.69  8.59  0.46
   32   42  0 #   18 | ....>G:...8_:[THY]T-----A[ADE]:..18_:H<....  0.88  0.80 21.14  8.77 -1.45
   33   41  0 #   19 | ....>G:...9_:[THY]T-----A[ADE]:..17_:H<....  0.88  0.29 20.88  8.50 -2.50
   34   40  0 #   20 | ....>G:..10_:[CYT]C-----G[GUA]:..16_:H<....  0.70  0.34 11.58  8.42 -0.03
   35   39  0 #   21 | ....>G:..11_:[CYT]C-----G[GUA]:..15_:H<....  0.82  0.56  5.73  8.42  0.22
   36   38  0 #   22 | ....>G:..12_:[THY]T-----A[ADE]:..14_:H<....  1.18  0.85  5.25  8.14  0.13
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 0 non-Watson-Crick base-pairs, and 2 helices (0 isolated bps)
##### Helix #1 (11): 1 - 11
##### Helix #2 (11): 12 - 22

[/color]
The output from running "analyze 1le5.inp" contains parameters in file '1le5.out'. For groove widths, you just need to consider one section:

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 GG/CC       ---       ---       ---       ---
   2 GG/CC       ---       ---       ---       ---
   3 GA/TC      10.2       ---      20.6       ---
   4 AA/TT       8.1       8.1      18.2      18.1
   5 AA/TT       9.2       9.2      16.6      16.1
   6 AT/AT      10.5      10.5      17.1      17.0
   7 TT/AA       9.6       9.5      18.9      18.8
   8 TC/GA      10.9       ---      22.6       ---
   9 CC/GG       ---       ---       ---       ---
  10 CT/AG       ---       ---       ---       ---
  11 TG/CA       ---       ---       ---       ---

Alternatively, you may manually extract only chains C and D, and repeat the above procedure.

HTH,

Xiang-Jun

Title: Re: This structure has broken O3' to P[i+1] linkages
Post by: Vandana on May 25, 2012, 08:20:39 am

Thankyou, I shall try the same again.


Regards
Vandana.R

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.