+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26768 | |||||||||
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Title | MicroED structure of Aeropyrum pernix protoglobin mutant | |||||||||
Map data | ||||||||||
Sample |
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Keywords | MicroED / protoglobin / heme / METAL BINDING PROTEIN | |||||||||
Function / homology | Protoglobin / Globin-sensor domain / Protoglobin / Globin/Protoglobin / Globin-like superfamily / oxygen binding / heme binding / Protogloblin ApPgb Function and homology information | |||||||||
Biological species | Aeropyrum pernix (archaea) | |||||||||
Method | electron crystallography / cryo EM | |||||||||
Authors | Danelius E / Gonen T / Unge JT | |||||||||
Funding support | United States, 2 items
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Citation | Journal: J Am Chem Soc / Year: 2022 Title: Biocatalytic Carbene Transfer Using Diazirines. Authors: Nicholas J Porter / Emma Danelius / Tamir Gonen / Frances H Arnold / Abstract: Biocatalytic carbene transfer from diazo compounds is a versatile strategy in asymmetric synthesis. However, the limited pool of stable diazo compounds constrains the variety of accessible products. ...Biocatalytic carbene transfer from diazo compounds is a versatile strategy in asymmetric synthesis. However, the limited pool of stable diazo compounds constrains the variety of accessible products. To overcome this restriction, we have engineered variants of protoglobin (Pgb) that use diazirines as carbene precursors. While the enhanced stability of diazirines relative to their diazo isomers enables access to a diverse array of carbenes, they have previously resisted catalytic activation. Our engineered Pgb variants represent the first example of catalysts for selective carbene transfer from these species at room temperature. The structure of an Pgb variant, determined by microcrystal electron diffraction (MicroED), reveals that evolution has enhanced access to the heme active site to facilitate this new-to-nature catalysis. Using readily prepared aryl diazirines as model substrates, we demonstrate the application of these highly stable carbene precursors in biocatalytic cyclopropanation, N-H insertion, and Si-H insertion reactions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26768.map.gz | 19 MB | EMDB map data format | |
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Header (meta data) | emd-26768-v30.xml emd-26768.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_26768.png | 68.1 KB | ||
Filedesc metadata | emd-26768.cif.gz | 5.7 KB | ||
Filedesc structureFactors | emd_26768_sf.cif.gz | 1011.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26768 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26768 | HTTPS FTP |
-Validation report
Summary document | emd_26768_validation.pdf.gz | 661.6 KB | Display | EMDB validaton report |
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Full document | emd_26768_full_validation.pdf.gz | 661.1 KB | Display | |
Data in XML | emd_26768_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | emd_26768_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26768 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26768 | HTTPS FTP |
-Related structure data
Related structure data | 7uteMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26768.map.gz / Format: CCP4 / Size: 25.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X: 0.51384 Å / Y: 0.48587 Å / Z: 0.50458 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L,...
Entire | Name: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L, Y60V, V63R, C102S, F145Q, I149L mutant |
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Components |
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-Supramolecule #1: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L,...
Supramolecule | Name: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L, Y60V, V63R, C102S, F145Q, I149L mutant type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Aeropyrum pernix (archaea) |
-Macromolecule #1: Protogloblin ApPgb
Macromolecule | Name: Protogloblin ApPgb / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Aeropyrum pernix (archaea) |
Molecular weight | Theoretical: 22.718887 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTPSDIPGYD YGRVEKSPIT DLEFDLLKKT VMLGEKDVMY LKKAGDVLKD QVDEILDLLV GWRASNEHLI YYFSNPDTGE PIKEYLERV RARFGAWILD TTSRDYNREW LDYQYEVGLR HHRSKKGVTD GVRTVPHIPL RYLIAQIYPL TATIKPFLAK K GGSPEDIE ...String: MTPSDIPGYD YGRVEKSPIT DLEFDLLKKT VMLGEKDVMY LKKAGDVLKD QVDEILDLLV GWRASNEHLI YYFSNPDTGE PIKEYLERV RARFGAWILD TTSRDYNREW LDYQYEVGLR HHRSKKGVTD GVRTVPHIPL RYLIAQIYPL TATIKPFLAK K GGSPEDIE GMYNAWFKSV VLQVAIWSHP YTKENDW UniProtKB: Protogloblin ApPgb |
-Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 4 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-Macromolecule #3: IMIDAZOLE
Macromolecule | Name: IMIDAZOLE / type: ligand / ID: 3 / Number of copies: 4 / Formula: IMD |
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Molecular weight | Theoretical: 69.085 Da |
Chemical component information | ChemComp-IMD: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 240 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Concentration | 20 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K / Max: 90.0 K |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 0.00025 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Camera length: 2460 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: PHENIX (ver. 1.20.1-4487-000) |
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Crystallography statistics | Number intensities measured: 33825 / Number structure factors: 33825 / Fourier space coverage: 72 / R merge: 0.43 / Overall phase residual: 0 / Phase error rejection criteria: not applicable / High resolution: 2.1 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.1 Å / Shell - Low resolution: 24.26 Å / Shell - Number structure factors: 33825 / Shell - Phase residual: 29.25 / Shell - Fourier space coverage: 72 / Shell - Multiplicity: 4.1 |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 18.2 / Target criteria: maximum likelihood |
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Output model | PDB-7ute: |