+Open data
-Basic information
Entry | Database: PDB / ID: 5k7r | ||||||
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Title | MicroED structure of trypsin at 1.7 A resolution | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.7 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 | 5k7r.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k7r.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k7r_validation.pdf.gz | 961.6 KB | Display | wwPDB validaton report |
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Full document | 5k7r_full_validation.pdf.gz | 966.2 KB | Display | |
Data in XML | 5k7r_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5k7r_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k7r ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k7r | HTTPS FTP |
-Related structure data
Related structure data | 8220MC 8216C 8217C 8218C 8219C 8221C 8222C 8472C 5k7nC 5k7oC 5k7pC 5k7qC 5k7sC 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/288 / 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
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has protein modification | Y | |
-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: Trypsin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.023354 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Bos taurus (cattle) | |||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||
Buffer component |
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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 / Date: Mar 11, 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: 1527 / Num. of grids imaged: 3 / Num. of real images: 1527 | ||||||||||||||||||||||||
Image scans | Sampling size: 0.0311999992 µm / Width: 2048 / Height: 2048 | ||||||||||||||||||||||||
EM diffraction | Camera length: 1500 mm | ||||||||||||||||||||||||
EM diffraction shell | Resolution: 1.7→1.79 Å / Fourier space coverage: 56.2 % / Multiplicity: 3.1 / Num. of structure factors: 1737 / Phase residual: 60.7 ° | ||||||||||||||||||||||||
EM diffraction stats | Fourier space coverage: 73.8 % / High resolution: 1.5 Å / Num. of intensities measured: 145833 / Num. of structure factors: 23542 / Phase error: 28.86 ° / Phase residual: 40.4 ° / Phase error rejection criteria: 0 / Rmerge: 0.773 / Rsym: 0.773 | ||||||||||||||||||||||||
Reflection | Resolution: 1.5→27.63 Å / Num. all: 145833 / Num. obs: 23542 / % possible obs: 73.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.773 / Rpim(I) all: 0.332 / Net I/σ(I): 2.3 | ||||||||||||||||||||||||
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: 53.12 Å / B: 56.08 Å / C: 64.38 Å / Space group name: P212121 / Space group num: 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.7 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2PTN Pdb chain-ID: A / Accession code: 2PTN / Pdb chain residue range: 16-245 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 1.7→25.86 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.86
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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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