Dear Thuy, For blob1 you should also try to fit alternative conformations. Your maps are good enough to give you a fair chance. You should also look for reasons behind these alternative conformations: has a neighboring disulfide bond partially opened? Is there a partially-occupied cadmium nearby? Is the substrate partially converted into product? Etc. From the static pictures without the neighborhood, we cannot deduce this for you.
Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von thuy ngo Gesendet: Donnerstag, 31. Oktober 2013 10:05 An: [email protected] Betreff: Re: [ccp4bb] help with strange density map Dear all, The gly104 sequence is correct. This is the substrate complex structure. In case of native structure, such strange of blob1 didnot appear Also for the second blob, I follow your suggestion and the result is nice I am still waitting for the suggestion of the first blob Thank you a lot, Sincerely yours On Thursday, October 31, 2013 4:45 PM, Prof. Dr. Arne Skerra <[email protected]<mailto:[email protected]>> wrote: Can you exclude a sequencing error for Gly104? Am 31.10.2013 um 08:40 schrieb thuy ngo: Dear all, I am dealing with two strange extra density map. One is connected from Cb of Proline to Ca of glycine (blob 1) and other is positioned between two symmetric molecules which is connected from Cb of Histidine to carboxylate group of Glutamate. I checked all the crystallization and purification condition but no ligand is suitable for these blobs. Could you suggest some possible candidates? This is the structure complex between peptide deformylase and fMAS Crystallization condition: 2M Sodium acetate, 0.1 M HEPES 7.5 and 0.05M CdSO4 Thank you <blob1_back.png><blob1_front.png><blob2.png> Prof. Dr. Arne Skerra Lehrstuhl f. Biologische Chemie | Technische Universitaet Muenchen Emil-Erlenmeyer-Forum 5 | 85350 Freising-Weihenstephan | Germany Phone: +49 (0)8161 71-4351 | Fax: -4352 eMail: [email protected]<mailto:[email protected]> | http://www.wzw.tum.de/bc
