Dear Yang Meiting, I have not solved protein - DNA complexes, but I have seen many protein densities with more or less ligand bound. When the ligand has a carboxylate group but doesn't bind tight enough, often an acetate or sulfate groups binds instead. Depending on how clear you see the phosphates and how sure you can be that there is not only solvent but some kind of covalently linked atoms between them, you should consider the disappointing case of e mere chain of sulfates or phosphates (depends on your crystallization conditions). If you can wash some crystals and detect DNA in them, that would be a good reasurance.
Best regards, Gottfried Am Freitag, den 17-12-2021 um 08:01 schrieb Petr Kolenko: Dear Yang Meiting, There are few things to know better about your structures first: 1) What is the resolution of the complex structure? 2) In what stage of structure refinement you are? Rwork/free would help. 3) Have you tried some automatic DNA building tools? I am not surprised that you can see only a fraction of DNA. I guess, solvent flattening may also decrease the visibility of this region. The only thing I would suggest now, do not expect to see the whole DNA immediately. Just start with the step-wise building if possible. The rest may appear in the later stage of model building. Best regards, Petr ________________________________________ From: CCP4 bulletin board on behalf of Meiting Yang Sent: Friday, December 17, 2021 7:29:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] the complex structure of protein and DNA Dear all， We have determined two Crystal structures, with one is apo structure and the other is a complex of the same protein with double-stranded DNA. In the complex, the protein structure is clearly viible, but the DNA only can be seen several phosphate groups. We want to know how do we get the complete DNA structure. The space group of the apo structure is P222, one asymmetric unit including two protein molecules. The space group of the complex structure is P2, one unit containing two protein molecules, 5 phosphate groups just situated near one protein molecules. The binding ability of the DNA and the protein is about 1 μM. The DNA we used for crystallization is 18 bp double-stranded DNA, but now only 5 phosphate groups can be observed. The crystal we have identified is a complex rather than a monomer, the cell parameters of complexes and monomers are different. Here, we want to get some suggestions, to get the complexe that contain the entire DNA structure. Best regards. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
