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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
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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
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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
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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.
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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
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