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- EMDB-30289: MicroED structure of anorthic Vancomycin at 1.05 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-30289
TitleMicroED structure of anorthic Vancomycin at 1.05 A resolution
Map data
Sample
  • Complex: Vancomycin
    • Protein or peptide: Vancomycin
  • Ligand: CHLORIDE ION
  • Ligand: water
KeywordsMicroED / Vancomycin / superbacteria / Antibiotic
Biological speciesAmycolatopsis orientalis (bacteria)
Methodelectron crystallography / cryo EM / Resolution: 1.05 Å
AuthorsFan Q / Zhou H
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)51925307 China
National Science Foundation (NSF, China)21733010 China
CitationJournal: 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
DepositionMay 18, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7c4v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30289.png

Downloads & links

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Map

FileDownload / File: emd_30289.map.gz / Format: CCP4 / Size: 16.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.26 Å/pix.
x 210 pix.
= 54.327 Å		0.26 Å/pix.
x 124 pix.
= 32.079 Å		0.26 Å/pix.
x 170 pix.
= 43.979 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.2587 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-2.1819685 - 12.975075
Average (Standard dev.)0.010650865 (±1.0030953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-114-126-163
Dimensions124170210
Spacing210124170
CellA: 54.327003 Å / B: 32.0788 Å / C: 43.979004 Å
α: 109.517 ° / β: 97.327 ° / γ: 106.58 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.25870.258701612903230.2587
M x/y/z210124170
origin x/y/z0.0000.0000.000
length x/y/z54.32732.07943.979
α/β/γ109.51797.327106.580
start NX/NY/NZ-163-114-126
NX/NY/NZ210124170
MAP C/R/S321
start NC/NR/NS-126-114-163
NC/NR/NS170124210
D min/max/mean-2.18212.9750.011

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Supplemental data

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Sample components

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Entire : Vancomycin

EntireName: Vancomycin
Components
  • Complex: Vancomycin
    • Protein or peptide: Vancomycin
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: Vancomycin

SupramoleculeName: Vancomycin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Amycolatopsis orientalis (bacteria)

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Macromolecule #1: Vancomycin

MacromoleculeName: Vancomycin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Amycolatopsis orientalis (bacteria)
Molecular weightTheoretical: 1.149977 KDa
SequenceString:
(MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG)

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 43 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 7
GridModel: Homemade / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 50 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average exposure time: 5.72 sec. / Average electron dose: 0.0286 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Camera length: 520 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.05 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: CCP4 package
Crystallography statisticsNumber intensities measured: 43720 / Number structure factors: 6462 / Fourier space coverage: 65.8 / R sym: 0.215 / R merge: 0.215 / Overall phase error: 0 / Overall phase residual: 1 / Phase error rejection criteria: 60 / High resolution: 1.05 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.05 Å / Shell - Low resolution: 1.1 Å / Shell - Number structure factors: 1907 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 66.9 / Shell - Multiplicity: 6.83

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Atomic model buiding 1

Initial modelPDB ID:

1fvm


Chain - Chain ID: A / Chain - Residue range: 4-7 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-7c4v:
MicroED structure of anorthic Vancomycin at 1.05 A resolution

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