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- PDB-6dkf: Caseinolytic protease (ClpP) from Staphylococcus aureus mutant - V7A -

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Basic information

Entry
Database: PDB / ID: 6dkf
TitleCaseinolytic protease (ClpP) from Staphylococcus aureus mutant - V7A
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Protease
Function / homologyATP-dependent Clp protease proteolytic subunit / ClpP, Ser active site / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / ClpP/crotonase-like domain superfamily / ClpP, histidine active site / Clp protease / Endopeptidase Clp serine active site. / Endopeptidase Clp histidine active site. / endopeptidase Clp / serine-type endopeptidase activity ...ATP-dependent Clp protease proteolytic subunit / ClpP, Ser active site / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / ClpP/crotonase-like domain superfamily / ClpP, histidine active site / Clp protease / Endopeptidase Clp serine active site. / Endopeptidase Clp histidine active site. / endopeptidase Clp / serine-type endopeptidase activity / cytoplasm / ATP-dependent Clp protease proteolytic subunit
Function and homology information
Specimen sourceStaphylococcus aureus subsp. aureus str. Newman (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsRipstein, Z.A. / Vahidi, S. / Kay, L.E. / Rubinstein, J.L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Reversible inhibition of the ClpP protease via an N-terminal conformational switch.
Authors: Siavash Vahidi / Zev A Ripstein / Massimiliano Bonomi / Tairan Yuwen / Mark F Mabanglo / Jordan B Juravsky / Kamran Rizzolo / Algirdas Velyvis / Walid A Houry / Michele Vendruscolo / John L Rubinstein / Lewis E Kay
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 29, 2018 / Release: Jun 27, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 27, 2018Structure modelrepositoryInitial release
1.1Jul 11, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Jul 25, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
B: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
A: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit


Theoretical massNumber of molelcules
Total (without water)301,11914
Polyers301,11914
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
ATP-dependent Clp protease proteolytic subunit / / Endopeptidase Clp


Mass: 21508.479 Da / Num. of mol.: 14 / Mutation: V7A
Source: (gene. exp.) Staphylococcus aureus subsp. aureus str. Newman (bacteria)
Strain: Newman / Gene: clpP, NWMN_0736 / Plasmid name: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) CodonPlus / References: UniProt: A6QF76, endopeptidase Clp

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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: Caseinolytic protease from Staphylococcus aureus (V7A)Endopeptidase Clp
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.301 MDa / Experimental value: YES
Source (natural)Organism: Staphylococcus aureus (strain Newman) (bacteria) / Strain: Newman
Source (recombinant)Organism: Escherichia coli Bl21(DE3) (bacteria) / Plasmid: pET24 / Strain: BL21(DE3) CodonPlus
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer ID
1100 mMpotassium chlorideKCl1
21 mMethylenediaminetetraacetic acidEDTA1
35 mMmagnesium chlorideMgCl21
45 %Igepal CA-6301
550 mMimidazole1
SpecimenConc.: 30 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: Modified Vitrobot

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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 / Nominal magnification: 75000 / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 43 e/Å2 / Details: movies were collected with 44 fractions / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 2 / Number of real images: 1837
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.8.2model fitting
9cryoSPARC0.5initial Euler assignment
10cryoSPARC0.5final Euler assignment
11cryoSPARCclassification
12cryoSPARC0.53D reconstruction
13PHENIX1.10.1-2155model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 878240
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 324522 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Atomic model building
IDPDB-IDPdb chain ID 3D fitting IDPdb chain residue range
13V5EA120-193
23QWDA120-193

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