6BBM | pdb_00006bbm

Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R5U
experimental model	PDB	3BH0

Sample
DnaB helicase - Lambda P helicase loader DNA replication complex
Sample Components
E coli DnaB helicase
Lambda P helicase loader

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge ...	3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	90883
Reported Resolution (Å)	4.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Relion was used to independently refine half sets using 0.143 gold-standard to a resolution of 4.1A. A total of 90,883 particles went into this recons ...	Relion was used to independently refine half sets using 0.143 gold-standard to a resolution of 4.1A. A total of 90,883 particles went into this reconstruction.
Refinement Type
Symmetry Type

Map-Model Fitting and Refinement
Id	1 (2R5U, 3BH0)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The initial fitting was done with the 2R5U and 3BH0 models onto which the E. coli amino sequence had been built. The linker segments that connected t ...	The initial fitting was done with the 2R5U and 3BH0 models onto which the E. coli amino sequence had been built. The linker segments that connected these segments were built by hand. PHENIX real_space_refine was used to refine the complete model for the B6P5 entity.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	8

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	-1
Maximum Defocus (nm)	-3
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	22500
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Preliminary grid screening was performed prior to Krios data collections. All microscope alignments were completed by the New York Structural Biology SEMC team.

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	Leginon	0.0
IMAGE ACQUISITION	Appion	0.0
IMAGE ACQUISITION	Appion	0.0
CTF CORRECTION	Gctf
MODEL FITTING	MOLREP
MODEL FITTING	Coot
SERIES ALIGNMENT	RELION
SERIES ALIGNMENT	Gautomatch
SERIES ALIGNMENT	EMAN2
RECONSTRUCTION	RELION
SERIES ALIGNMENT	TOMO3D
SERIES ALIGNMENT	Dynamo
SERIES ALIGNMENT	EMAN2
RECONSTRUCTION	Dynamo
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF correction was performed before data processing on summed micrographs using Gctf.

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.