+Open data
-Basic information
Entry | Database: PDB / ID: 8sbb | ||||||
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Title | Cryo-EM structure of FtAlkB | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Enzyme | ||||||
Function / homology | Alkane/xylene monooxygenase / Fatty acid desaturase domain / Fatty acid desaturase / monooxygenase activity / lipid metabolic process / plasma membrane / DODECANE / : / Alkane 1-monooxygenase Function and homology information | ||||||
Biological species | Fontimonas thermophila (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å | ||||||
Authors | Zhang, J. / Feng, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure and mechanism of the alkane-oxidizing enzyme AlkB. Authors: Xue Guo / Jianxiu Zhang / Lei Han / Juliet Lee / Shoshana C Williams / Allison Forsberg / Yan Xu / Rachel Narehood Austin / Liang Feng / Abstract: Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase ...Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase (AlkB), a membrane-spanning metalloenzyme, converts straight chain alkanes to alcohols in the first step of the microbially-mediated degradation of alkanes, thereby playing a critical role in the global cycling of carbon and the bioremediation of oil. AlkB biodiversity is attributed to its ability to oxidize alkanes of various chain lengths, while individual AlkBs target a relatively narrow range. Mechanisms of substrate selectivity and catalytic activity remain elusive. Here we report the cryo-EM structure of AlkB, which provides a distinct architecture for membrane enzymes. Our structure and functional studies reveal an unexpected diiron center configuration and identify molecular determinants for substrate selectivity. These findings provide insight into the catalytic mechanism of AlkB and shed light on its function in alkane-degrading microorganisms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sbb.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sbb.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 8sbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sbb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8sbb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8sbb_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 8sbb_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/8sbb ftp://data.pdbj.org/pub/pdb/validation_reports/sb/8sbb | HTTPS FTP |
-Related structure data
Related structure data | 40303MC 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
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 45569.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fontimonas thermophila (bacteria) / Gene: SAMN04488120_1209 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I2KHB9 | ||||
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#2: Antibody | Mass: 14502.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||
#3: Chemical | #4: Chemical | ChemComp-D12 / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: FtAklB-Nanobody / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||
Buffer solution | pH: 7 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107776 / Symmetry type: POINT | ||||||||||||||||||||||||
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