+Open data
-Basic information
Entry | Database: PDB / ID: 5k7s | ||||||
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Title | MicroED structure of proteinase K at 1.6 A resolution | ||||||
Components | Proteinase K | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Engyodontium album (fungus) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.6 Å | ||||||
Authors | de la Cruz, M.J. / Hattne, J. / Shi, D. / Seidler, P. / Rodriguez, J. / Reyes, F.E. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Gonen, T. | ||||||
Citation | Journal: Nat Methods / Year: 2017 Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen / Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography. | ||||||
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 | 5k7s.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k7s.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 5k7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k7s_validation.pdf.gz | 202.1 KB | Display | wwPDB validaton report |
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Full document | 5k7s_full_validation.pdf.gz | 201.6 KB | Display | |
Data in XML | 5k7s_validation.xml.gz | 722 B | Display | |
Data in CIF | 5k7s_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k7s ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k7s | HTTPS FTP |
-Related structure data
Related structure data | 8221MC 8216C 8217C 8218C 8219C 8220C 8222C 8472C 5k7nC 5k7oC 5k7pC 5k7qC 5k7rC 5k7tC 5ty4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/28 / Data set type: diffraction image data / Details: SB Data Grid |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K | ||
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#2: Chemical | #3: 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: Proteinase K / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.028938 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Engyodontium album (fungus) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 25 mg/ml / 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 / Date: Mar 7, 2016 | ||||||||||||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM | ||||||||||||||||||||||||
Electron lens | Mode: DIFFRACTION | ||||||||||||||||||||||||
Specimen holder | Cryogen: NITROGEN | ||||||||||||||||||||||||
Image recording | Average exposure time: 4.1 sec. / Electron dose: 0.004 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 295 / Num. of grids imaged: 1 / Num. of real images: 295 | ||||||||||||||||||||||||
Image scans | Sampling size: 0.0311999992 µm / Width: 2048 / Height: 2048 | ||||||||||||||||||||||||
EM diffraction | Camera length: 1200 mm | ||||||||||||||||||||||||
EM diffraction shell | Resolution: 1.6→1.64 Å / Fourier space coverage: 85.8 % / Multiplicity: 5.7 / Num. of structure factors: 1857 / Phase residual: 53.1 ° | ||||||||||||||||||||||||
EM diffraction stats | Fourier space coverage: 81.1 % / High resolution: 1.3 Å / Num. of intensities measured: 302892 / Num. of structure factors: 46369 / Phase error: 24.33 ° / Phase residual: 32.2 ° / Phase error rejection criteria: 0 / Rmerge: 0.728 / Rsym: 0.728 | ||||||||||||||||||||||||
Reflection | Resolution: 1.3→20.75 Å / Num. all: 302892 / Num. obs: 46369 / % possible obs: 81.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.728 / Rpim(I) all: 0.295 / Net I/σ(I): 2.4 | ||||||||||||||||||||||||
Reflection shell |
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-Processing
Software | Name: PHENIX / Version: (1.10_2155: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 67.6 Å / B: 67.6 Å / C: 101.36 Å / Space group name: P43212 / Space group num: 96 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5I9S Pdb chain-ID: A / Pdb chain residue range: 1-279 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 1.6→20.751 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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