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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.
DescriptorIsoaspartyl dipeptidase (E.C.3.4.19.-)
KeywordsHYDROLASE / Designed protein filament / Hydrolase / Isoaspartyl Dipeptidase
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (10.5 Å resolution / Filament / Single particle)
AuthorsGarcia-Seisdedos, H. / Empereur-Mot, C. / Elad, N. / Levy, E.D.
CitationNature, 2017, 548, 244-247

Nature, 2017, 548, 244-247 Yorodumi Papers
Proteins evolve on the edge of supramolecular self-assembly.
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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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: Polypeptide(L)
Isoaspartyl dipeptidase


Mass: 41167.758 Da / Num. of mol.: 12
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P39377, EC: 3.4.19.-

Cellular component

Molecular function

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

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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 / Strain: K12
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' / Plasmid: pET-30a(+)
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMTris-HClC4H12CINO31
2100mMSodium 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 FIELD / 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
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1EMAN2.1PARTICLE SELECTION1
2RELION1.4IMAGE ACQUISITION1
3EMAN2.1IMAGE ACQUISITION1
5CTFFIND3.0CTF CORRECTION1
8UCSF Chimera1.10.2MODEL FITTING1
10RELION1.4INITIAL EULER ASSIGNMENT1
11RELION1.4FINAL EULER ASSIGNMENT1
12RELION1.4CLASSIFICATION1
13RELION1.4RECONSTRUCTION1
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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