6V8R | pdb_00006v8r

Proteinase K Determined by MicroED Phased by ARCIMBOLDO_SHREDDER

• PDB DOI: https://doi.org/10.2210/pdb6V8R/pdb
• EM Map EMD-21109: EMDB EMDataResource

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


• Deposited: 2019-12-11 Released: 2020-08-12 
• Deposition Author(s): Richards, L.S., Martynowycz, M.W., Sawaya, M.R., Millan, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Department of Energy (DOE, United States), Sao Paulo Research Foundation (FAPESP), Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.60 Å
• R-Value Free: 
  0.232 (Depositor) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Richards, L.R., Millan, C., Miao, J., Martynowycz, M.W., Sawaya, M.R., Gonen, T., Borges, R.J., Uson, I., Rodriguez, J.A.

(2020) Acta Crystallogr D Biol Crystallogr 76: 703-712

• DOI: https://doi.org/10.1107/S2059798320008049

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: 29.04 kDa 
• Atom Count: 2,176 
• 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 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:  0.232 (Depositor) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.25	α = 90
b = 67.25	β = 90
c = 99.92	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Arcimboldo	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Richards, L.S., Martynowycz, M.W., Sawaya, M.R., Millan, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5T32GM008496
National Science Foundation (NSF, United States)	United States	DMR-1548924
Department of Energy (DOE, United States)	United States	DE-FC02-02ER63421
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM128867
Sao Paulo Research Foundation (FAPESP)	Brazil	16/24191-8
Sao Paulo Research Foundation (FAPESP)	Brazil	17/13485-3
Spanish Ministry of Economy and Competitiveness	Spain	BIO2015-64216-P
Spanish Ministry of Economy and Competitiveness	Spain	PGC2018-101370-B-100
Spanish Ministry of Economy and Competitiveness	Spain	MDM2014-0435-01

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary