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Questions and answers => General discussions (Q&As) => Topic started by: mon_sharma on January 14, 2013, 03:09:29 pm

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Title: Analyzing some pdb files of bent DNA
Post by: mon_sharma on January 14, 2013, 03:09:29 pm
Hello,
I was trying the web 3DNA interface to analyze the bent DNA for pdbid: 2O8B.pdb or 2O8C.pdb. The local base pair step parameters at the site of non canonical base pair are shown as ----. Also Guanine is designated as 'g', not 'G'. Is there some problem with pdb file or something is not recognized by 3DNA?

Thank you in advance
Regards
Monika
Title: Re: Analyzing some pdb files of bent DNA
Post by: xiangjun on January 14, 2013, 04:22:19 pm
Thanks for using w3DNA, a web-service hosted and supported by the Olson laboratory at Rutgers University. w3DNA aims to make commonly/routinely used 3DNA functionality easily available. To taking full advantage of 3DNA, the standard command-line version is the way to go. Also, w3DNA is still using 3DNA v2.0, while the the command-line version is v2.1.

The issue you experienced for PDB entries 2o8b and 2o8c, i.e., some step parameters are designated as "----", is due to the kink in the two structures. Thus, find_pair now takes each DNA as two helical regions instead of a continuous helix, see below:
find_pair 2o8b.pdb 2o8b.inp
# contents of 2o8b.inp
2o8b.pdb
2o8b.out
    2         # duplex
   15         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   30  0 #    1 | ....>E:...1_:[.DG]G-----C[.DC]:..30_:F<....  1.14  0.36 14.09  9.30 -0.44
    2   29  0 #    2 | ....>E:...2_:[.DA]A-----T[.DT]:..29_:F<....  0.89  0.82 26.82  9.09 -1.13
    3   28  0 #    3 | ....>E:...3_:[.DA]A-----T[.DT]:..28_:F<....  0.23  0.03 18.38  9.24 -3.78
    4   27  0 #    4 | ....>E:...4_:[.DC]C-----G[.DG]:..27_:F<....  0.78  0.19  8.59  8.93 -3.40
    5   26  0 #    5 | ....>E:...5_:[.DC]C-----G[.DG]:..26_:F<....  0.56  0.29 17.33  9.24 -3.00
    6   25  0 #    6 | ....>E:...6_:[.DG]G-----C[.DC]:..25_:F<....  0.29  0.27 19.28  9.01 -3.20
    7   24  9 #    7 x ....>E:...7_:[.DC]C-----G[.DG]:..24_:F<....  0.22  0.01 24.18  9.04 -3.55
    8   23  0 #    8 | ....>E:...8_:[.DG]G-**--T[.DT]:..23_:F<....  5.22  0.31 43.28  9.87  7.00
    9   22  0 #    9 | ....>E:...9_:[.DC]C-----G[.DG]:..22_:F<....  0.44  0.33 20.98  8.84 -2.85
   10   21  0 #   10 | ....>E:..10_:[.DG]G-----C[.DC]:..21_:F<....  0.41  0.39 10.80  9.05 -3.28
   11   20  0 #   11 | ....>E:..11_:[.DC]C-----G[.DG]:..20_:F<....  0.26  0.01 12.86  9.06 -4.07
   12   19  0 #   12 | ....>E:..12_:[.DT]T-----A[.DA]:..19_:F<....  0.85  0.47 11.88  8.95 -2.62
   13   18  0 #   13 | ....>E:..13_:[.DA]A-----T[.DT]:..18_:F<....  0.53  0.18  9.30  8.85 -3.65
   14   17  0 #   14 | ....>E:..14_:[.DG]G-----C[.DC]:..17_:F<....  1.17  0.94 21.28  8.97 -0.89
   15   16  0 #   15 | ....>E:..15_:[.DG]G-----C[.DC]:..16_:F<....  1.17  0.05 37.85  8.66 -1.83
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 1 non-Watson-Crick base-pair, and 2 helices (0 isolated bps)
##### Helix #1 (7 ): 1 - 7
##### Helix #2 (8 ): 8 - 15

You can fix the problem by either changing 9 for bp #7 to 0, or running analyze with the -c option:
Code: [Select]
analyze -c 2o8b.inp
In 3DNA, lower case a/c/g/t/u is used for modified bases of A/C/G/T/U respectively. For example, in 2o8c, 6OG is assigned as g.

HTH,

Xiang-Jun


Title: Re: Analyzing some pdb files of bent DNA
Post by: mon_sharma on January 15, 2013, 11:30:57 am
Thank you Dr.Xiang-Jun. I was wondering how the kinks or breaks are defined in 3DNA. There are 4 such similar bent DNA pdbs: 2O8B, 2O8C, 2O8D and 2O8E. The kinks were seem to be identified in the first 3 and not the last one. Structurally superimposing at the kinked area, no such significant visual differences were observed. So, how the breaks were identified in the first three and not the last. I am missing something here, I think.
Title: Re: Analyzing some pdb files of bent DNA
Post by: xiangjun on January 15, 2013, 12:15:40 pm
The helix break is controlled by a parameter callled helix_break in file $X3DNA/config/misc_3dna.par:

Code: [Select]
#   distance criterion for helix break
<helix_break>7.5</helix_break>
It has a default value of 7.5 Å. Reset it to a larger value, e.g. 8.0 Å (see FAQs), will do the trick for all your cases.

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University