+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8222 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MicroED structure of thermolysin at 2.5 A resolution | |||||||||
Map data | Thermolysin | |||||||||
Sample |
| |||||||||
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 / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | de la Cruz MJ / Hattne J | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8222.map.gz | 2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8222-v30.xml emd-8222.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_8222.png | 302.6 KB | ||
Filedesc metadata | emd-8222.cif.gz | 5.7 KB | ||
Filedesc structureFactors | emd_8222_sf.cif.gz | 1.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8222 | HTTPS FTP |
-Related structure data
Related structure data | 5k7tMC 8216C 8217C 8218C 8219C 8220C 8221C 8472C 5k7nC 5k7oC 5k7pC 5k7qC 5k7rC 5k7sC 5ty4C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_8222.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Thermolysin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.80759 Å / Y: 0.80759 Å / Z: 0.82371 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Thermolysin
Entire | Name: Thermolysin |
---|---|
Components |
|
-Supramolecule #1: Thermolysin
Supramolecule | Name: Thermolysin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Bacillus thermoproteolyticus (bacteria) |
Molecular weight | Theoretical: 34.634 KDa |
-Macromolecule #1: Thermolysin
Macromolecule | Name: Thermolysin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: thermolysin |
---|---|
Source (natural) | Organism: Bacillus thermoproteolyticus (bacteria) |
Molecular weight | Theoretical: 34.360336 KDa |
Sequence | String: ITGTSTVGVG RGVLGDQKNI NTTYSTYYYL QDNTRGNGIF TYDAKYRTTL PGSLWADADN QFFASYDAPA VDAHYYAGVT YDYYKNVHN RLSYDGNNAA IRSSVHYSQG YNNAFWNGSQ MVYGDGDGQT FIPLSGGIDV VAHELTHAVT DYTAGLIYQN E SGAINEAI ...String: ITGTSTVGVG RGVLGDQKNI NTTYSTYYYL QDNTRGNGIF TYDAKYRTTL PGSLWADADN QFFASYDAPA VDAHYYAGVT YDYYKNVHN RLSYDGNNAA IRSSVHYSQG YNNAFWNGSQ MVYGDGDGQT FIPLSGGIDV VAHELTHAVT DYTAGLIYQN E SGAINEAI SDIFGTLVEF YANKNPDWEI GEDVYTPGIS GDSLRSMSDP AKYGDPDHYS KRYTGTQDNG GVHINSGIIN KA AYLISQG GTHYGVSVVG IGRDKLGKIF YRALTQYLTP TSNFSQLRAA AVQSATDLYG STSQEVASVK QAFDAVGVK UniProtKB: Thermolysin |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA |
---|---|
Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: DIMETHYL SULFOXIDE
Macromolecule | Name: DIMETHYL SULFOXIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: DMS |
---|---|
Molecular weight | Theoretical: 78.133 Da |
Chemical component information | ChemComp-DMS: |
-Macromolecule #5: ISOPROPYL ALCOHOL
Macromolecule | Name: ISOPROPYL ALCOHOL / type: ligand / ID: 5 / Number of copies: 1 / Formula: IPA |
---|---|
Molecular weight | Theoretical: 60.095 Da |
Chemical component information | ChemComp-IPA: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 21 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 Component:
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1750 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 3 / Number real images: 721 / Number diffraction images: 721 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Crystallography statistics | Number intensities measured: 224846 / Number structure factors: 25029 / Fourier space coverage: 58.5 / R sym: 0.634 / R merge: 0.634 / Overall phase error: 26.44 / Overall phase residual: 44.76 / Phase error rejection criteria: 0 / High resolution: 1.6 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.5 Å / Shell - Low resolution: 2.75 Å / Shell - Number structure factors: 2741 / Shell - Phase residual: 47.2 / Shell - Fourier space coverage: 96.8 / Shell - Multiplicity: 12.2 |
---|---|
Molecular replacement | Software - Name: MOLREP (ver. 11.4.05) / Software - details: Starting model PDB ID 2tli |
Symmetry determination software list | Software - Name: POINTLESS (ver. 1.10.21) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
Merging software list | Software - Name: AIMLESS (ver. 0.5.25) |