[English] 日本語
Yorodumi- EMDB-30288: MicroED structure of orthorhombic Vancomycin at 1.2 A resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30288 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MicroED structure of orthorhombic Vancomycin at 1.2 A resolution | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Amycolatopsis orientalis (bacteria) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.2 Å | |||||||||
Authors | Fan Q / Zhou H / Li X / Wang J | |||||||||
Funding support | China, 2 items
| |||||||||
Citation | Journal: Angew Chem Int Ed Engl / Year: 2020 Title: Precise Control Over Kinetics of Molecular Assembly: Production of Particles with Tunable Sizes and Crystalline Forms. Authors: Qingrui Fan / Linhai Li / Han Xue / Heng Zhou / Lishan Zhao / Jie Liu / Junqiang Mao / Shuwang Wu / Shizhong Zhang / Chenyang Wu / Xueming Li / Xin Zhou / Jianjun Wang / Abstract: It has been long-pursued but remains a challenge to precisely manipulate the molecular assembly process to obtain desired functional structures. Reported here is the control over the assembly of ...It has been long-pursued but remains a challenge to precisely manipulate the molecular assembly process to obtain desired functional structures. Reported here is the control over the assembly of solute molecules, by a programmed recrystallization of solvent crystal grains, to form micro/nanoparticles with tunable sizes and crystalline forms. A quantitative correlation between the protocol of recrystallization temperature and the assembly kinetics results in precise control over the size of assembled particles, ranging from single-atom catalysts, pure drug nanoparticles, to sub-millimeter organic-semiconductor single crystals. The extensive regulation of the assembly rates leads to the unique and powerful capability of tuning the stacking of molecules, involving the formation of single crystals of notoriously crystallization-resistant molecules and amorphous structures of molecules with a very high propensity to crystallize, which endows it with wide-ranging applications. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30288.map.gz | 4.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30288-v30.xml emd-30288.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_30288.png | 62.7 KB | ||
Filedesc structureFactors | emd_30288_sf.cif.gz | 195.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30288 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30288 | HTTPS FTP |
-Validation report
Summary document | emd_30288_validation.pdf.gz | 435 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30288_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | emd_30288_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | emd_30288_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30288 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30288 | HTTPS FTP |
-Related structure data
Related structure data | 7c4uMC 7c4vC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30288.map.gz / Format: CCP4 / Size: 5.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.27861 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Vancomycin
Entire | Name: Vancomycin |
---|---|
Components |
|
-Supramolecule #1: Vancomycin
Supramolecule | Name: Vancomycin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Amycolatopsis orientalis (bacteria) |
-Macromolecule #1: Vancomycin
Macromolecule | Name: Vancomycin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Amycolatopsis orientalis (bacteria) |
Molecular weight | Theoretical: 1.149977 KDa |
Sequence | String: (MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG) |
-Macromolecule #3: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL |
---|---|
Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 50 / 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 |
---|---|
Grid | Model: Homemade / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 50 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average exposure time: 5.72 sec. / Average electron dose: 0.0286 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Camera length: 730 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
---|---|
Crystal parameters | Unit cell - A: 20.06 Å / Unit cell - B: 33.02 Å / Unit cell - C: 41.72 Å / Unit cell - γ: 90.00 ° / Unit cell - α: 90.00 ° / Unit cell - β: 90.00 ° / Space group: P 2 21 21 |
Crystallography statistics | Number intensities measured: 64605 / Number structure factors: 6840 / Fourier space coverage: 74.7 / R sym: 0.185 / R merge: 0.185 / Overall phase error: 0 / Overall phase residual: 1 / Phase error rejection criteria: 60 / High resolution: 1.2 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.2 Å / Shell - Low resolution: 1.3 Å / Shell - Number structure factors: 1907 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 75.6 / Shell - Multiplicity: 7.45 |