+Open data
-Basic information
Entry | Database: PDB / ID: 8wyx | ||||||
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Title | Partially closed falcilysin, from free falcilysin dataset | ||||||
Components | Falcilysin | ||||||
Keywords | HYDROLASE / falcilysin partially closed conformation | ||||||
Function / homology | Function and homology information hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / protein processing / metalloendopeptidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Lin, J.Q. / Yan, X.F. / Lescar, J. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: To Be Published Title: Partially closed falcilysin, from free falcilysin dataset Authors: Lin, J.Q. / Yan, X.F. / Lescar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wyx.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wyx.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 8wyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wyx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8wyx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8wyx_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 8wyx_validation.cif.gz | 57.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/8wyx ftp://data.pdbj.org/pub/pdb/validation_reports/wy/8wyx | HTTPS FTP |
-Related structure data
Related structure data | 37940MC 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: 132220.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: FLN / Production host: Escherichia coli (E. coli) / References: UniProt: Q76NL8 |
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#2: Chemical | ChemComp-ZN / |
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: Falcilysin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 / Details: 20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21.1_5286 / Category: model refinement |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50355 / Symmetry type: POINT |
Refinement | Cross valid method: NONE |