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Yorodumi- PDB-5a3e: 2.5A structure of lysozyme determined by MicroED with data from a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a3e | ||||||
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Title | 2.5A structure of lysozyme determined by MicroED with data from a single crystal | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / MICROED | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.501 Å | ||||||
Authors | Nannenga, B.L. / Shi, D. / Leslie, A.G.W. / Gonen, T. | ||||||
Citation | Journal: Nat Methods / Year: 2014 Title: High-resolution structure determination by continuous-rotation data collection in MicroED. Authors: Brent L Nannenga / Dan Shi / Andrew G W Leslie / Tamir Gonen / Abstract: MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called 'continuous ...MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called 'continuous rotation'. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallographic software tool MOSFLM, which resulted in improved resolution for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biology. | ||||||
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 | 5a3e.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a3e.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 5a3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a3e ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a3e | HTTPS FTP |
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-Related 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 / Source method: isolated from a natural source / Details: EGG WHITES / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1 |
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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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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Crystal grow | pH: 4.5 / Details: pH 4.5 |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Image recording | Film or detector model: GENERIC CCD |
Diffraction | Mean temperature: 100 K |
Detector | Date: Feb 5, 2014 |
Radiation | Scattering type: electron |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→11.2 Å / Num. obs: 3116 / % possible obs: 80.1 % / Redundancy: 3.4 % |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.292 / % possible all: 80.1 |
-Processing
Software |
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3D reconstruction | Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3J6K Resolution: 2.501→11.189 Å / SU ML: 0.23 / σ(F): 1.46 / Phase error: 21.2 / 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 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→11.189 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5006→11.1887 Å
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