+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8219 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MicroED structure of thaumatin at 2.5 A resolution | |||||||||
Map data | Thaumatin | |||||||||
Sample |
| |||||||||
Function / homology | Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / cytoplasmic vesicle / Thaumatin I Function and homology information | |||||||||
Biological species | Thaumatococcus daniellii (katemfe) / Katemfe (katemfe) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | de la Cruz MJ / Hattne J / Shi D / Seidler P / Rodriguez J / Reyes FE / Sawaya MR / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8219.map.gz | 1.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8219-v30.xml emd-8219.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_8219.png | 169.7 KB | ||
Filedesc structureFactors | emd_8219_sf.cif.gz | 852 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8219 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8219 | HTTPS FTP |
-Related structure data
Related structure data | 5k7qMC 8216C 8217C 8218C 8220C 8221C 8222C 8472C 5k7nC 5k7oC 5k7pC 5k7rC 5k7sC 5k7tC 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 |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_8219.map.gz / Format: CCP4 / Size: 1.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Thaumatin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.8072 Å / Y: 0.8072 Å / Z: 0.85402 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 92 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Thaumatin
Entire | Name: Thaumatin |
---|---|
Components |
|
-Supramolecule #1: Thaumatin
Supramolecule | Name: Thaumatin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Thaumatococcus daniellii (katemfe) |
Molecular weight | Theoretical: 22.166 KDa |
-Macromolecule #1: Thaumatin-1
Macromolecule | Name: Thaumatin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Katemfe (katemfe) |
Molecular weight | Theoretical: 22.227059 KDa |
Sequence | String: ATFEIVNRCS YTVWAAASKG DAALDAGGRQ LNSGESWTIN VEPGTNGGKI WARTDCYFDD SGSGICKTGD CGGLLRCKRF GRPPTTLAE FSLNQYGKDY IDISNIKGFN VPMNFSPTTR GCRGVRCAAD IVGQCPAKLK APGGGCNDAC TVFQTSEYCC T TGKCGPTE ...String: ATFEIVNRCS YTVWAAASKG DAALDAGGRQ LNSGESWTIN VEPGTNGGKI WARTDCYFDD SGSGICKTGD CGGLLRCKRF GRPPTTLAE FSLNQYGKDY IDISNIKGFN VPMNFSPTTR GCRGVRCAAD IVGQCPAKLK APGGGCNDAC TVFQTSEYCC T TGKCGPTE YSRFFKRLCP DAFSYVLDKP TTVTCPGSSN YRVTFCPTA |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 18 / 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 / Component - Concentration: 1.1 M / Component - Name: ammonium tartate |
---|---|
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: 2000 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 / Digitization - Sampling interval: 0.0311999992 µm / Number grids imaged: 3 / Number real images: 471 / Number diffraction images: 471 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Crystal parameters | Unit cell - A: 57.78 Å / Unit cell - B: 57.78 Å / Unit cell - C: 149.70 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 41 21 2 |
---|---|
Crystallography statistics | Number intensities measured: 51116 / Number structure factors: 12786 / Fourier space coverage: 81.5 / R sym: 0.434 / R merge: 0.434 / Overall phase error: 28.74 / Overall phase residual: 41.7 / Phase error rejection criteria: 0 / High resolution: 2.11 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.5 Å / Shell - Low resolution: 2.86 Å / Shell - Number structure factors: 2825 / Shell - Phase residual: 52.4 / Shell - Fourier space coverage: 92.2 / Shell - Multiplicity: 3.9 |
Molecular replacement | Software - Name: MOLREP (ver. 11.4.05) / Software - details: Starting model PDB ID 4ek0 |
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) |