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Yorodumi- PDB-6law: MicroED structure of proteinase K at 1.50A determained using crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6law | |||||||||||||||
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Title | MicroED structure of proteinase K at 1.50A determained using crystal lamellas prepared by focused ion beam milling | |||||||||||||||
Components | Proteinase K | |||||||||||||||
Keywords | HYDROLASE / Proteinase K / MicroED / Focused Ion Beam / crystal lamella | |||||||||||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Parengyodontium album (fungus) | |||||||||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.5 Å | |||||||||||||||
Authors | Zhou, H. / Luo, Z. / Li, X. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: J Struct Biol / Year: 2019 Title: Using focus ion beam to prepare crystal lamella for electron diffraction. Authors: Heng Zhou / Zhipu Luo / Xueming Li / Abstract: Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the ...Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation. These observations provide important information to optimize the FIB milling, and hence is important to obtain high-quality crystal samples for routine structure determination of protein crystals using the electron cryo-microscope. | |||||||||||||||
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 | 6law.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6law.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 6law.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6law ftp://data.pdbj.org/pub/pdb/validation_reports/la/6law | HTTPS FTP |
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-Related structure data
Related structure data | 0865MC 0864C 6lavC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-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: proteinase K / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Parengyodontium album (fungus) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 0.028 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
EM diffraction | Camera length: 1000 mm |
EM diffraction shell | Resolution: 1.5→1.55 Å / Fourier space coverage: 90.6 % / Multiplicity: 5.2 / Num. of structure factors: 3693 / Phase residual: 1 ° |
EM diffraction stats | Fourier space coverage: 91.1 % / High resolution: 1.5 Å / Num. of intensities measured: 200471 / Num. of structure factors: 37742 / Phase error: 0 ° / Phase residual: 1 ° / Phase error rejection criteria: 60 / Rmerge: 0.245 / Rsym: 0.245 |
Detector | Date: Apr 21, 2018 |
-Processing
Software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 69.31 Å / B: 69.31 Å / C: 104.12 Å / Space group name: P43212 / Space group num: 96 | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 1.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | ||||||||||||||||||||||||
Refinement | Resolution: 1.5→12.31 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.195 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 71.5 Å2 / Biso mean: 10.998 Å2 / Biso min: 3.37 Å2
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Refinement step | Cycle: final / Resolution: 1.5→12.31 Å
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LS refinement shell | Resolution: 1.5→1.538 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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