2BK2 | pdb_00002bk2

The prepore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PFO

Sample
PNEUMOLYSIN

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	PLUNGED INTO ETHANE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	223
Reported Resolution (Å)	28
Resolution Method
Other Details	RESIDUES 134-142 ARE MISSING FROM THE SEQUENCE. THE 31-MER CAN BE GENERATED BY APPLYING 31-FOLD ROTATIONAL SYMMETRY
Refinement Type
Symmetry Type	POINT
Point Symmetry	C31

Map-Model Fitting and Refinement
Id	1 (1PFO)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--THE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998, CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1106). THE ...	METHOD--THE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998, CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1106). THE ALPHA CARBON TRACE OF PERFRINGOLYSIN 0 WAS MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO THE POSITION OF ONE SUBUNIT. THE BEST FIT WAS OBTAINED BY SEPARATING THE MONOMER INTO TWO RIGID BODIES- DOMAINS 1-3 (36-390) AND DOMAIN 4 (391-500). THE COMPLETE OLIGOMER (31-MER) WAS GENERATED AND CHECKED FOR CLOSE CONTACTS BOTH BY EYE AND USING THE CCP4 PROGRAM CONTACT.

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	100
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1100
Maximum Defocus (nm)	3200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	42000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	PHASE FLIPPING

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.