7C4V | pdb_00007c4v

MicroED structure of anorthic Vancomycin at 1.05 A resolution


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.05 Å
  • R-Value Free: 
    0.268 (Depositor) 
  • R-Value Work: 
    0.232 (Depositor) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7C4V

This is version 1.4 of the entry. See complete history

Literature

Precise Control Over Kinetics of Molecular Assembly: Production of Particles with Tunable Sizes and Crystalline Forms.

Fan, Q.Li, L.Xue, H.Zhou, H.Zhao, L.Liu, J.Mao, J.Wu, S.Zhang, S.Wu, C.Li, X.Zhou, X.Wang, J.

(2020) Angew Chem Int Ed Engl 59: 15141-15146

  • DOI: https://doi.org/10.1002/anie.202003922
  • Primary Citation Related Structures: 
    7C4U, 7C4V

  • PubMed 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 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.


  • Organizational Affiliation
    • Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.

Macromolecule Content 

  • Total Structure Weight: 2.98 kDa 
  • Atom Count: 246 
  • Modeled Residue Count: 14 
  • Deposited Residue Count: 14 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vancomycin
A, B
7Amycolatopsis orientalisMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
vancosamine-(1-2)-beta-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G14263HU
GlyCosmos: G14263HU

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
3FG
Query on 3FG
A, B
L-PEPTIDE LINKINGC8 H9 N O4

--

GHP
Query on GHP
A, B
D-PEPTIDE LINKINGC8 H9 N O3

--

MLU
Query on MLU
A, B
D-PEPTIDE LINKINGC7 H15 N O2

--

OMY
Query on OMY
A, B
L-PEPTIDE LINKINGC9 H10 Cl N O4TYR
OMZ
Query on OMZ
A, B
D-PEPTIDE LINKINGC9 H10 Cl N O4

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.05 Å
  • R-Value Free:  0.268 (Depositor) 
  • R-Value Work:  0.232 (Depositor) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 13.97α = 109.52
b = 18.55β = 97.33
c = 23.86γ = 106.58
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China51925307
National Science Foundation (NSF, China)China21733010

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Data collection
  • Version 1.2: 2020-08-26
    Changes: Data collection
  • Version 1.3: 2021-03-17
    Changes: Database references
  • Version 1.4: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description