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- PDB-7c4u: MicroED structure of orthorhombic Vancomycin at 1.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 7c4u
TitleMicroED structure of orthorhombic Vancomycin at 1.2 A resolution
ComponentsVancomycin
KeywordsANTIBIOTIC / MicroED / Vancomycin / superbacteria
Function / homologyVancomycin
Function and homology information
Biological speciesAmycolatopsis orientalis (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.2 Å
AuthorsFan, Q. / Zhou, H. / Li, X. / Wang, J.
Funding support China, 2items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Data collection
Category: pdbx_entity_branch_descriptor / pdbx_entity_branch_link
Revision 1.2Aug 26, 2020Group: Data collection / Category: pdbx_entity_branch_descriptor
Revision 1.3Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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  • EMDB-30288
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Assembly

Deposited unit
A: Vancomycin
B: Vancomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,9825
Polymers2,3002
Non-polymers6823
Water90150
1
A: Vancomycin
hetero molecules


  • defined by author&software
  • 1.51 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,5093
Polymers1,1501
Non-polymers3592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-7 kcal/mol
Surface area1400 Å2
MethodPISA
2
B: Vancomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4732
Polymers1,1501
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint2 kcal/mol
Surface area1410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)20.060, 33.020, 41.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein/peptide Vancomycin / /


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 vancosamine-(1-2)-beta-D-glucopyranose /


Type: oligosaccharide, Glycopeptide / Class: Antibiotic / Mass: 323.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4.
References: Vancomycin
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Vancomycin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Amycolatopsis orientalis (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 50 % / Chamber temperature: 298 K

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 5.72 sec. / Electron dose: 0.0286 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM diffractionCamera length: 730 mm
EM diffraction shellResolution: 1.2→1.3 Å / Fourier space coverage: 75.6 % / Multiplicity: 7.45 / Num. of structure factors: 1907 / Phase residual: 1 °
EM diffraction statsFourier space coverage: 74.7 % / High resolution: 1.2 Å / Num. of intensities measured: 64605 / Num. of structure factors: 6840 / Phase error: 0 ° / Phase residual: 1 ° / Phase error rejection criteria: 60 / Rmerge: 0.185 / Rsym: 0.185
DetectorDate: Jun 1, 2019
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 7.45 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1907 / CC1/2: 0.781 / % possible all: 75.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
EM software
IDNameCategory
6CCP4 packagemodel fitting
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 20.06 Å / B: 33.02 Å / C: 41.72 Å / Space group name: P22121 / Space group num: 18
CTF correctionType: NONE
3D reconstructionMethod: CRYSTALLOGRAPHY / Resolution: 1.2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL
Atomic model buildingPDB-ID: 1FVM

1fvm


Pdb chain-ID: A / Pdb chain residue range: 1-7
RefinementResolution: 1.2→7.571 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 342 5 %Random selection
Rwork0.202 6497 --
obs0.2027 6839 75.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 32.72 Å2 / Biso mean: 11.4269 Å2 / Biso min: 4.42 Å2
Refinement stepCycle: final / Resolution: 1.2→7.57 Å
LigandSolventTotal
Num. atoms43 50 253
Biso mean10.18 18.86 -
Num. residues--14
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.50970.2741680.2408320276
1.5097-7.57090.19981740.1905329575

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