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Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: Damien on November 21, 2012, 09:15:42 am

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Title: O3'-P distance too long after reconstruction
Post by: Damien on November 21, 2012, 09:15:42 am
Dear Xiangjun,

I analyzed the DNA molecule contained in PDB 2AOR from Web 3DNA. I then downloaded the parameter file. And I performed a reconstruction from the parameter file.

The resulting structure build.pdb contains many O3'-P bonds having a too long length, up to 4 A.

May you tell me what I made wrong ?

Many thanks for your help

Damien
Title: Re: O3'-P distance too long after reconstruction
Post by: xiangjun on November 21, 2012, 10:31:54 am
Hi Damien,

The fact that "O3'-P distance too long after reconstruction" is well expected; 3DNA built structures are accurate for the bases, with only an approximate sugar-phosphate backbone. See FAQ "How do I build nucleic acid structures with sugar-phosphate backbone? (http://forum.x3dna.org/faqs/how-do-i-build-nucleic-acid-structures-with-sugar-phosphate-backbone/)"

For cases with longer than the default 4.5 A O3'(i)--P(i+1) distance, the 3DNA rebuild program outputs info message as below (using your example, and with a B-DNA backbone conformation):

Code: [Select]
O3' (#317) and P (#331) on chain A have distance 5.3 over 4.5: no linkage assigned
O3' (#768) and P (#782) on chain B have distance 5.2 over 4.5: no linkage assigned

This approximate structure may serve as a starting point for energy minimization.

Xiang-Jun
 
Title: Re: O3'-P distance too long after reconstruction
Post by: Damien on November 21, 2012, 11:07:01 am
Many many thanks Xiang-Jun for this prompt reply! I appreciate!

OK, I understand the approximation for the sugar-phosphate backbone.

I have two questions:

- The default O3'-P distance is 4.5A. From the ADIT server of the PDB, the expected value is 1.6A. What is in fact the range of the possible values?

- Could you indicate some tools alllowing to do energy minimization?

Thanks again,

Damien
Title: Re: O3'-P distance too long after reconstruction
Post by: xiangjun on November 21, 2012, 11:20:27 am
Quote
- The default O3'-P distance is 4.5A. From the ADIT server of the PDB, the expected value is 1.6A. What is in fact the range of the possible values?
The O3'-P covalent bond distance is ~1.6 A, as you noticed on the ADIT server of the PDB. The 3DNA default of 4.5 A is purely an empirical value used to decide if to include the bond in a corresponding CONECT record in the rebuilt PDB file; it has no 'chemical' meaning. Have a look of build.pdb file using a text editor, you will see my point.

Quote
- Could you indicate some tools alllowing to do energy minimization?
AMBER should help. Some other MD packages or Phenix should also do the trick. Yet, I still failed to find a command-line tool that can 'regularize' the backbone to a reasonable geometry while keeping the base atoms fixed.

HTH,

Xiang-Jun

Title: Re: O3'-P distance too long after reconstruction
Post by: Damien on November 21, 2012, 11:23:40 am
Many thanks Xiang-Jun for your help! I appreciate!

Damien
Title: Re: O3'-P distance too long after reconstruction
Post by: xiangjun on September 06, 2013, 05:13:48 pm
Update on 2013-09-06: please see my post titled "Restraint optimization of DNA backbone geometry using PHENIX (http://x3dna.org/highlights/restraint-optimization-of-dna-backbone-geometry-using-phenix)" for a PHENIX-based method to solve the long O3'-P distance problem.

Xiang-Jun

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.