+Open data
-Basic information
Entry | Database: PDB / ID: 3j4g | ||||||
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Title | Structure of lysozyme solved by MicroED to 2.9 A | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Shi, D. / Nannenga, B.L. / Iadanza, M.G. / Gonen, T. | ||||||
Citation | Journal: Elife / Year: 2013 Title: Three-dimensional electron crystallography of protein microcrystals. Authors: Dan Shi / Brent L Nannenga / Matthew G Iadanza / Tamir Gonen / Abstract: We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme ...We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1-1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name 'MicroED', that may have wide applicability in structural biology. DOI: http://dx.doi.org/10.7554/eLife.01345.001. | ||||||
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 | 3j4g.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j4g.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 3j4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j4g_validation.pdf.gz | 851.6 KB | Display | wwPDB validaton report |
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Full document | 3j4g_full_validation.pdf.gz | 863.1 KB | Display | |
Data in XML | 3j4g_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 3j4g_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/3j4g ftp://data.pdbj.org/pub/pdb/validation_reports/j4/3j4g | HTTPS FTP |
-Related structure data
Related structure data | 2945MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: lysozyme / Type: COMPLEX |
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Buffer solution | Name: 50 mM sodium acetate, 3.5 M sodium choride, 15% PEG 5000 pH: 4.5 Details: 50 mM sodium acetate, 3.5 M sodium choride, 15% PEG 5000 |
Specimen | Conc.: 200 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jul 1, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 0.1 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.901→54.447 Å / Num. all: 2717 / Num. obs: 2499 |
-Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||
Refinement | Resolution: 2.901→19.25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8311 / SU ML: 0.3 / σ(F): 1.47 / Phase error: 22.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 58.03 Å2 / Biso mean: 26.0779 Å2 / Biso min: 1.47 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.901→19.25 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON CRYSTALLOGRAPHY / Total num. of bins used: 2
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