+Open data
-Basic information
Entry | Database: PDB / ID: 5k7t | ||||||
---|---|---|---|---|---|---|---|
Title | MicroED structure of thermolysin at 2.5 A resolution | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 2.5 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5k7t.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5k7t.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 5k7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k7t_validation.pdf.gz | 916.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5k7t_full_validation.pdf.gz | 919.9 KB | Display | |
Data in XML | 5k7t_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 5k7t_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k7t ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k7t | HTTPS FTP |
-Related structure data
Related structure data | 8222MC 8216C 8217C 8218C 8219C 8220C 8221C 8472C 5k7nC 5k7oC 5k7pC 5k7qC 5k7rC 5k7sC 5ty4C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/290 / Data set type: diffraction image data / Details: SB Data Grid |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
---|
-Non-polymers , 5 types, 28 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-IPA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
---|---|
EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Thermolysin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.034634 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Bacillus thermoproteolyticus (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
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 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Microscopy | Model: FEI TECNAI F20 | ||||||||||||||||||||||||
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: 721 / Num. of grids imaged: 3 / Num. of real images: 721 | ||||||||||||||||||||||||
Image scans | Sampling size: 0.0311999992 µm / Width: 2048 / Height: 2048 | ||||||||||||||||||||||||
EM diffraction | Camera length: 1750 mm | ||||||||||||||||||||||||
EM diffraction shell | Resolution: 2.5→2.75 Å / Fourier space coverage: 96.8 % / Multiplicity: 12.2 / Num. of structure factors: 2741 / Phase residual: 47.2 ° | ||||||||||||||||||||||||
EM diffraction stats | Fourier space coverage: 58.5 % / High resolution: 1.6 Å / Num. of intensities measured: 224846 / Num. of structure factors: 25029 / Phase error: 26.44 ° / Phase residual: 44.76 ° / Phase error rejection criteria: 0 / Rmerge: 0.634 / Rsym: 0.634 | ||||||||||||||||||||||||
Reflection | Resolution: 1.6→30.14 Å / Num. all: 224846 / Num. obs: 25029 / % possible obs: 58.5 % / Redundancy: 9 % / Rmerge(I) obs: 0.634 / Rpim(I) all: 0.219 / Net I/σ(I): 4 | ||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software | Name: PHENIX / Version: (1.10_2155: ???) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 120 ° / A: 90.75 Å / B: 90.75 Å / C: 126.13 Å / Space group name: P6122 / Space group num: 178 | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2TLI Pdb chain-ID: A / Accession code: 2TLI / Pdb chain residue range: 1-316 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.5→30.135 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.44 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|