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- PDB-8jgm: Cryo-EM sturcutre of DANGEROUS MIX 3 (DM3) from Hohenlieth (Hh-0) -

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Basic information

Entry
Database: PDB / ID: 8jgm
TitleCryo-EM sturcutre of DANGEROUS MIX 3 (DM3) from Hohenlieth (Hh-0)
ComponentsDM3Hh0
KeywordsHYDROLASE / Complex / Polymorphism / Hybrid necrosis
Function / homology: / Peptidase S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / peptidase activity / Alpha/Beta hydrolase fold / proteolysis / DM3Hh0
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsKim, G. / Song, J.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1A2B5B03001517 Korea, Republic Of
CitationJournal: To Be Published
Title: Cryo-EM sturcutre of DANGEROUS MIX 3 (DM3) from Hohenlieth (Hh-0)
Authors: Kim, G. / Song, J.J.
History
DepositionMay 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DM3Hh0
B: DM3Hh0
C: DM3Hh0
D: DM3Hh0
E: DM3Hh0
F: DM3Hh0


Theoretical massNumber of molelcules
Total (without water)302,4896
Polymers302,4896
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
DM3Hh0 / DANGGEROUS MIX 3 / DM3


Mass: 50414.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Variant: Hohenlieth accession (Hh-0) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A068LMZ4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DANGGEROUS MIX 3 (DM3) from Hohenlieth accession (Hh-0)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium cholorideNaCl1
250 mMTrisamineTris1
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid treated by graphene oxide prior to use / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 413056 / Symmetry type: POINT

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