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- PDB-5lp3: Three tetrameric rings of Isoaspartyl Dipeptidase fitted in an EM... -

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Basic information

Entry
Database: PDB / ID: 5lp3
TitleThree tetrameric rings of Isoaspartyl Dipeptidase fitted in an EM volume.
ComponentsIsoaspartyl dipeptidase
KeywordsHYDROLASE / Designed protein filament / Hydrolase / Isoaspartyl Dipeptidase
Function / homologyPeptidase M38, beta-aspartyl dipeptidase / Amidohydrolase-related / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolase / Isoaspartyl-dipeptidase / Amidohydrolase family / Omega peptidases / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / beta-aspartyl-peptidase activity / metallopeptidase activity ...Peptidase M38, beta-aspartyl dipeptidase / Amidohydrolase-related / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolase / Isoaspartyl-dipeptidase / Amidohydrolase family / Omega peptidases / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / beta-aspartyl-peptidase activity / metallopeptidase activity / zinc ion binding / cytosol / cytoplasm / Isoaspartyl dipeptidase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 10.5 Å resolution
AuthorsGarcia-Seisdedos, H. / Empereur-Mot, C. / Elad, N. / Levy, E.D.
CitationJournal: Nature / Year: 2017
Title: Proteins evolve on the edge of supramolecular self-assembly.
Authors: Hector Garcia-Seisdedos / Charly Empereur-Mot / Nadav Elad / Emmanuel D Levy
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 11, 2016 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 16, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Aug 23, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
B: Isoaspartyl dipeptidase
C: Isoaspartyl dipeptidase
D: Isoaspartyl dipeptidase
E: Isoaspartyl dipeptidase
A: Isoaspartyl dipeptidase
F: Isoaspartyl dipeptidase
G: Isoaspartyl dipeptidase
H: Isoaspartyl dipeptidase
I: Isoaspartyl dipeptidase
J: Isoaspartyl dipeptidase
K: Isoaspartyl dipeptidase
L: Isoaspartyl dipeptidase


Theoretical massNumber of molelcules
Total (without water)494,01312
Polyers494,01312
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)37540
ΔGint (kcal/M)-188
Surface area (Å2)140370
MethodPISA

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Components

#1: Protein/peptide
Isoaspartyl dipeptidase


Mass: 41167.758 Da / Num. of mol.: 12 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: iadA, yjiF, b4328, JW4291 / Production host: Escherichia coli (E. coli) / References: UniProt: P39377, Omega peptidases

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Isoaspartyl Dipeptidase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Plasmid: pET-30a(+)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTris-HClC4H12CINO31
2100 mMSodium ChlorideNaCl1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 297 kelvins

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / C2 aperture diameter: 30 mm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2RELION1.4image acquisition
3EMAN2.1image acquisition
5CTFFIND3.0CTF correction
8UCSF Chimera1.10.2model fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Particles were manually selected from filaments only
Number of particles selected: 38786
SymmetryPoint symmetry: D4
3D reconstructionResolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 17277 / Details: 2 CLASSES WERE MERGED IN THE FINAL RECONSTRUCTION / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

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