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- PDB-5lij: polyalanine chain built in bacteriophage phi812K1-420 cement prot... -

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Basic information

Entry
Database: PDB / ID: 5lij
Titlepolyalanine chain built in bacteriophage phi812K1-420 cement protein density map
Componentspolyalanine chain built in bacteriophage phi812K1-420 cement protein density map
KeywordsVIRAL PROTEIN / polyvalent staphylococcal bactoriophage / Myoviridae / tail sheath / tail contraction / viral protein
Specimen sourceStaphylococcus phage 812 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsNovacek, J. / Siborova, M. / Benesik, M. / Pantucek, R. / Doskar, J. / Plevka, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate.
Authors: Jiří Nováček / Marta Šiborová / Martin Benešík / Roman Pantůček / Jiří Doškař / Pavel Plevka
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 14, 2016 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collectionem_software_em_software.name / _em_software.version

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Assembly

Deposited unit
P: polyalanine chain built in bacteriophage phi812K1-420 cement protein density map


Theoretical massNumber of molelcules
Total (without water)10,8221
Polyers10,8221
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)9430

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Components

#1: Protein/peptide polyalanine chain built in bacteriophage phi812K1-420 cement protein density map


Mass: 10821.817 Da / Num. of mol.: 1
Source: (gene. exp.) Staphylococcus phage 812 (bacteriophage)
Production host: Staphylococcaceae (bacteria)

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Staphylococcus phage 812 / Type: VIRUS / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus phage 812 (bacteriophage) / Strain: K420
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Staphylococcus aureus
Virus shellDiameter: 1100 nm / Triangulation number (T number): 16
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
150 mMtrisTrisHCl1
210 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl21
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 100 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.86 sec. / Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
11JALIGNinitial Euler assignment
12JALIGNfinal Euler assignment
14RELIONclassification
15J3DR3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12018 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL

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