+Open data
-Basic information
Entry | Database: PDB / ID: 7c4v | |||||||||
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Title | MicroED structure of anorthic Vancomycin at 1.05 A resolution | |||||||||
Components | Vancomycin | |||||||||
Keywords | ANTIBIOTIC / MicroED / Vancomycin / superbacteria | |||||||||
Function / homology | Vancomycin Function and homology information | |||||||||
Biological species | Amycolatopsis orientalis (bacteria) | |||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 1.05 Å | |||||||||
Authors | Fan, Q. / Zhou, H. / Li, X. / Wang, J. | |||||||||
Funding support | China, 2items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7c4v.cif.gz | 24.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c4v.ent.gz | 15.2 KB | Display | PDB format |
PDBx/mmJSON format | 7c4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c4v_validation.pdf.gz | 973.2 KB | Display | wwPDB validaton report |
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Full document | 7c4v_full_validation.pdf.gz | 979.8 KB | Display | |
Data in XML | 7c4v_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 7c4v_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/7c4v ftp://data.pdbj.org/pub/pdb/validation_reports/c4/7c4v | HTTPS FTP |
-Related structure data
Related structure data | 30289MC 7c4uC 1fvmS |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. Source: (natural) Amycolatopsis orientalis (bacteria) / References: Vancomycin #2: Polysaccharide | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Compound details | VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...VANCOMYCIN | Has ligand of interest | Y | |
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-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: Vancomycin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Amycolatopsis orientalis (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Homemade |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 50 % / Chamber temperature: 298 K |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Average exposure time: 5.72 sec. / Electron dose: 0.0286 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
EM diffraction | Camera length: 520 mm |
EM diffraction shell | Resolution: 1.05→1.1 Å / Fourier space coverage: 66.9 % / Multiplicity: 6.83 / Num. of structure factors: 1907 / Phase residual: 1 ° |
EM diffraction stats | Fourier space coverage: 65.8 % / High resolution: 1.05 Å / Num. of intensities measured: 43720 / Num. of structure factors: 6462 / Phase error: 0 ° / Phase residual: 1 ° / Phase error rejection criteria: 60 / Rmerge: 0.215 / Rsym: 0.215 |
Detector | Date: Jun 1, 2019 |
Reflection shell | Resolution: 1.05→1.1 Å / Redundancy: 6.83 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.04 / Num. unique obs: 852 / CC1/2: 0.949 / % possible all: 66.9 |
-Processing
Software |
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EM software |
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EM 3D crystal entity | ∠α: 109.52 ° / ∠β: 97.33 ° / ∠γ: 106.58 ° / A: 13.97 Å / B: 18.55 Å / C: 23.86 Å / Space group name: P1 / Space group num: 1 | ||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||
3D reconstruction | Method: CRYSTALLOGRAPHY / Resolution: 1.05 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL | ||||||||||||||||||||
Atomic model building | PDB-ID: 1FVM Pdb chain-ID: A / Accession code: 1FVM / Pdb chain residue range: 4-7 / Source name: PDB / Type: experimental model | ||||||||||||||||||||
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FVM Resolution: 1.05→7.875 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 30.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||
Displacement parameters | Biso max: 25.63 Å2 / Biso mean: 8.8747 Å2 / Biso min: 3.23 Å2 | ||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.05→7.88 Å
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LS refinement shell | Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / % reflection Rfree: 5 %
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