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- EMDB-7951: cryo-EM density map of ClpP from Staphylococcus aureus with bound... -

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Basic information

Entry
Database: EMDB / ID: 7951
Titlecryo-EM density map of ClpP from Staphylococcus aureus with bound Acyldepsipeptide (V7A mutant)
Map data
SampleCaseinolytic protease from Staphylococcus aureusEndopeptidase Clp:
SourceStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / 5.6 Å resolution
AuthorsRipstein ZA / Vahidi S / Kay LE / Rubinstein JL
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
DateDeposition: May 29, 2018 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jul 25, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.38
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.38
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7951.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.45 Å/pix.
= 232. Å
160 pix
1.45 Å/pix.
= 232. Å
160 pix
1.45 Å/pix.
= 232. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:0.38 (by author), 0.38 (movie #1):
Minimum - Maximum-0.58350974 - 1.3202851
Average (Standard dev.)0.005069425 (0.07511473)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin0.0.0.
Limit159.159.159.
Spacing160160160
CellA=B=C: 232.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z232.000232.000232.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.5841.3200.005

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Supplemental data

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Sample components

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Entire Caseinolytic protease from Staphylococcus aureus

EntireName: Caseinolytic protease from Staphylococcus aureus / Number of components: 2

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Component #1: protein, Caseinolytic protease from Staphylococcus aureus

ProteinName: Caseinolytic protease from Staphylococcus aureusEndopeptidase Clp
Recombinant expression: No
MassExperimental: 301 kDa
SourceSpecies: Staphylococcus aureus (bacteria) / Strain: Newman
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET24 / Strain: BL21(DE3) CodonPlus

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Component #2: protein, Caseinolytic protease from Staphylococcus aureus

ProteinName: Caseinolytic protease from Staphylococcus aureusEndopeptidase Clp
Recombinant expression: No
SourceSpecies: Staphylococcus aureus (bacteria) / Strain: Newman
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 30 mg/ml / pH: 7
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temperature: 277 K / Humidity: 100 % / Details: Modified Vitrobot.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000. X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 75

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D7 (2*7 fold dihedral) / Number of projections: 37133
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF

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