+Open data
-Basic information
Entry | Database: PDB / ID: 8eum | |||||||||
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Title | MicroED structure of an Aeropyrum pernix protoglobin mutant | |||||||||
Components | Protogloblin ApPgb | |||||||||
Keywords | METAL BINDING PROTEIN / MicroED / protoglobin / directed evolution | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aeropyrum pernix (archaea) | |||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Danelius, E. / Gonen, T. / Unge, J.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Am Chem Soc / Year: 2023 Title: MicroED Structure of a Protoglobin Reactive Carbene Intermediate. Authors: Emma Danelius / Nicholas J Porter / Johan Unge / Frances H Arnold / Tamir Gonen / Abstract: Microcrystal electron diffraction (MicroED) is an emerging technique that has shown great potential for describing new chemical and biological molecular structures. Several important structures of ...Microcrystal electron diffraction (MicroED) is an emerging technique that has shown great potential for describing new chemical and biological molecular structures. Several important structures of small molecules, natural products, and peptides have been determined using methods. However, only a couple of novel protein structures have thus far been derived by MicroED. Taking advantage of recent technological advances, including higher acceleration voltage and using a low-noise detector in counting mode, we have determined the first structure of an protoglobin (Pgb) variant by MicroED using an AlphaFold2 model for phasing. The structure revealed that mutations introduced during directed evolution enhance carbene transfer activity by reorienting an α helix of Pgb into a dynamic loop, making the catalytic active site more readily accessible. After exposing the tiny crystals to the substrate, we also trapped the reactive iron-carbenoid intermediate involved in this engineered Pgb's new-to-nature activity, a challenging carbene transfer from a diazirine via a putative metallo-carbene. The bound structure discloses how an enlarged active site pocket stabilizes the carbene bound to the heme iron and, presumably, the transition state for the formation of this key intermediate. This work demonstrates that improved MicroED technology and the advancement in protein structure prediction now enable investigation of structures that was previously beyond reach. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eum.cif.gz | 265.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eum.ent.gz | 200.7 KB | Display | PDB format |
PDBx/mmJSON format | 8eum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/8eum ftp://data.pdbj.org/pub/pdb/validation_reports/eu/8eum | HTTPS FTP |
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-Related structure data
Related structure data | 28615MC 8eunC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
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