5D9C
Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data)
Summary for 5D9C
| Entry DOI | 10.2210/pdb5d9c/pdb |
| Related | 5D9B 5D9D |
| Descriptor | Luciferin regenerating enzyme, MAGNESIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total) |
| Functional Keywords | beta-prooeller, hydrolase |
| Biological source | Photinus pyralis (Common eastern firefly) |
| Total number of polymer chains | 1 |
| Total formula weight | 34745.37 |
| Authors | Yamashita, K.,Pan, D.,Okuda, T.,Murai, T.,Kodan, A.,Yamaguchi, T.,Gomi, K.,Kajiyama, N.,Kato, H.,Ago, H.,Yamamoto, M.,Nakatsu, T. (deposition date: 2015-08-18, release date: 2015-09-23, Last modification date: 2023-09-06) |
| Primary citation | Yamashita, K.,Pan, D.,Okuda, T.,Sugahara, M.,Kodan, A.,Yamaguchi, T.,Murai, T.,Gomi, K.,Kajiyama, N.,Mizohata, E.,Suzuki, M.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Park, J.,Song, C.,Hatsui, T.,Yabashi, M.,Iwata, S.,Kato, H.,Ago, H.,Yamamoto, M.,Nakatsu, T. An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. Sci Rep, 5:14017-14017, 2015 Cited by PubMed Abstract: Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection. PubMed: 26360462DOI: 10.1038/srep14017 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.6 Å) |
Structure validation
Download full validation report
