6N4U | pdb_00006n4u

MicroED structure of Proteinase K at 2.75A resolution from a single milled crystal.

• PDB DOI: https://doi.org/10.2210/pdb6N4U/pdb
• EM Map EMD-0343: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Expression System: Parengyodontium album
• Mutation(s): No 


• Deposited: 2018-11-20 Released: 2019-02-06 
• Deposition Author(s): Martynowycz, M.W., Zhao, W., Hattne, J., Jensen, G.J., Gonen, T.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.75 Å
• R-Value Free: 
  0.263 (Depositor) 
• R-Value Work: 
  0.238 (Depositor) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Collection of Continuous Rotation MicroED Data from Ion Beam-Milled Crystals of Any Size.

Martynowycz, M.W., Zhao, W., Hattne, J., Jensen, G.J., Gonen, T.

(2019) Structure 27: 545-548.e2

• PubMed: 30661853 
• DOI: https://doi.org/10.1016/j.str.2018.12.003
• Primary Citation Related Structures: 
  6N4U


• PubMed Abstract: 
  

  Microcrystal electron diffraction (MicroED) allows for macromolecular structure solution from nanocrystals. To create crystals of suitable size for MicroED data collection, sample preparation typically involves sonication or pipetting a slurry of crystals from a crystallization drop. The resultant crystal fragments are fragile and the quality of the data that can be obtained from them is sensitive to subsequent sample preparation for cryoelectron microscopy as interactions in the water-air interface can damage crystals during blotting. Here, we demonstrate the use of a focused ion beam to generate lamellae of macromolecular protein crystals for continuous rotation MicroED that are of ideal thickness, easy to locate, and require no blotting optimization. In this manner, crystals of nearly any size may be scooped and milled to desired dimensions prior to data collection, thus streamlining the methodology for sample preparation for MicroED.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.14 kDa 
• Atom Count: 2,057 
• Modeled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	279	Parengyodontium album	Mutation(s): 0  Gene Names: PROK EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.75 Å
• R-Value Free:  0.263 (Depositor) 
• R-Value Work:  0.238 (Depositor) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.46	α = 90
b = 67.46	β = 90
c = 106.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.14

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Martynowycz, M.W., Zhao, W., Hattne, J., Jensen, G.J., Gonen, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R35 GM122588

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary