5K7S | pdb_00005k7s

MicroED structure of proteinase K at 1.6 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5K7S/pdb
• EM Map EMD-8221: EMDB EMDataResource

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


• Deposited: 2016-05-26 Released: 2017-04-05 
• Deposition Author(s): de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Eisenberg, D., Gonen, T.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.60 Å
• R-Value Free: 
  0.255 (Depositor) 
• R-Value Work: 
  0.224 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.

de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Weiss, S.C., Kim, S.K., Hinck, C.S., Hinck, A.P., Calero, G., Eisenberg, D., Gonen, T.

(2017) Nat Methods 14: 399-402

• PubMed: 28192420 
• DOI: https://doi.org/10.1038/nmeth.4178
• Primary Citation Related Structures: 
  5K7N, 5K7O, 5K7P, 5K7Q, 5K7R, 5K7S, 5K7T, 5TY4


• PubMed Abstract: 
  

  Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA.
Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry, Chemistry &Biochemistry, and Molecular Biology Institute, UCLA, Los Angeles, California, USA.
Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.01 kDa 
• Atom Count: 2,252 
• 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  EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.60 Å
• R-Value Free:  0.255 (Depositor) 
• R-Value Work:  0.224 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/289

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.059	α = 90
b = 67.059	β = 90
c = 100.713	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.10_2155

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Eisenberg, D., Gonen, T.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2018-08-22
  Changes: Data collection, Database references
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary