+Open data
-Basic information
Entry | Database: PDB / ID: 7kns | ||||||||||||
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Title | Cryo-EM structure of jack bean urease | ||||||||||||
Components | Urease | ||||||||||||
Keywords | HYDROLASE / urease | ||||||||||||
Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / metabolic process / nickel cation binding / toxin activity Similarity search - Function | ||||||||||||
Biological species | Canavalia ensiformis (jack bean) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å | ||||||||||||
Authors | Feathers, J.R. / Spoth, K.A. / Fromme, J.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J Struct Biol X / Year: 2021 Title: Experimental evaluation of super-resolution imaging and magnification choice in single-particle cryo-EM. Authors: J Ryan Feathers / Katherine A Spoth / J Christopher Fromme / Abstract: The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In ...The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In principle, super-resolution imaging should enable reconstructions to surpass the physical Nyquist limit by increasing sampling frequency, yet there are few reports of reconstructions that do so. Here we directly examine the contribution of super-resolution information, obtained with the K3 direct electron detector using a 2-condenser microscope, to single-particle cryo-EM reconstructions surpassing the physical Nyquist limit. We also present a comparative analysis of a sample imaged at four different magnifications. This analysis demonstrates that lower magnifications can be beneficial, despite the loss of higher resolution signal, due to the increased number of particle images obtained. To highlight the potential utility of lower magnification data collection, we produced a 3.5 Å reconstruction of jack bean urease with particles from a single micrograph. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kns.cif.gz | 803.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kns.ent.gz | 686.6 KB | Display | PDB format |
PDBx/mmJSON format | 7kns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kns_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7kns_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7kns_validation.xml.gz | 129.3 KB | Display | |
Data in CIF | 7kns_validation.cif.gz | 201.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/7kns ftp://data.pdbj.org/pub/pdb/validation_reports/kn/7kns | HTTPS FTP |
-Related structure data
Related structure data | 20016MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10547 (Title: Jack bean urease imaged at 49kX nominal magnification Data size: 169.3 / Data #1: Super resolution movies [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 90902.625 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P07374, urease #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-PO4 / Has ligand of interest | N | |
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-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: Jack bean urease / Type: COMPLEX / Entity ID: #1 / Source: NATURAL | |||||||||||||||||||||||||
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Source (natural) | Organism: Canavalia ensiformis (jack bean) | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56038 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3LA4 |