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Author Topic: 3IGK and Tilt value  (Read 2042 times)

Offline prasun30

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3IGK and Tilt value
« on: November 11, 2016, 08:42:28 am »
Dear Forum

I am encountering a peculiar problem while running 3DNA for PDB ID: 3IGK.
Since, it has only single strand, I downloaded the biological assembly and used it.

I am appending the local basepair steps:

Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 GG/CC      0.89     -0.38      3.53      4.20      0.53     33.47
   2 GC/GC     -0.63     -0.31      3.36     -2.73     -0.93     38.79
   3 CA/TG      3.12     -3.38      2.07   -174.43     -5.33    108.92
   4 AT/AT     -1.54     -0.00      3.10     11.53     -0.00    -75.14
   5 TG/CA     -0.07      3.65      3.47     -3.19      4.47      3.50
   6 GC/GC      0.63     -0.31      3.36      2.73     -0.93     38.79
   7 CC/GG     -0.89     -0.38      3.53     -4.20      0.53     33.47
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.      0.22     -0.16      3.20    -23.73     -0.24     25.97
      s.d.      1.53      2.04      0.52     66.68      2.89     54.85
****************************************************************************

Please have a look at tilt value for the serial number 3 CA/TG step.
Can somebody guide me regarding the possible reasoning behind it.

Regards
Prasun

Offline xiangjun

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Re: 3IGK and Tilt value
« Reply #1 on: November 11, 2016, 11:35:03 am »
Hi Prasun,

Thanks for posting your 3DNA-related questions on the Forum. Your case is yet another example of how "weird" parameters can be obtained when non-Watson-Crick base-pairs are involved. In your case it is the two Hoogsteen T-A pairs, as shown below.

****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.032) ...1>B:...3_:[.DG]G-----C[.DC]:..10_:B<...2 (0.025)     |
   2   (0.029) ...1>B:...4_:[.DG]G-----C[.DC]:...9_:B<...2 (0.026)     |
   3   (0.018) ...1>B:...5_:[.DC]C-----G[.DG]:...8_:B<...2 (0.043)     |
   4   (0.030) ...1>B:...6_:[.DA]A-**+-T[.DT]:...7_:B<...2 (0.026)     |
   5   (0.026) ...1>B:...7_:[.DT]T-**+-A[.DA]:...6_:B<...2 (0.030)     |

   6   (0.043) ...1>B:...8_:[.DG]G-----C[.DC]:...5_:B<...2 (0.018)     |
   7   (0.026) ...1>B:...9_:[.DC]C-----G[.DG]:...4_:B<...2 (0.029)     |
   8   (0.025) ...1>B:..10_:[.DC]C-----G[.DG]:...3_:B<...2 (0.032)     |

Note: This structure contains 2[2] non-Watson-Crick base-pairs.


In such cases, you may find the 'simple' base-pair and step parameters introduced in 3DNA v2.3 more 'intuitive'.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.