9OYY | pdb_00009oyy

MicroED structure of proteinase K from microcrystals frozen by traditional cryoEM methods

PDB DOI: https://doi.org/10.2210/pdb9OYY/pdb

Classification: HYDROLASE
Organism(s): Parengyodontium album
Mutation(s): Yes

Deposited: 2025-06-04 Released: 2026-07-01
Deposition Author(s): Vlahakis, N., Summers, J.A., Rodriguez, J.A., Dahlberg, P., Wakatsuki, S.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 2.20 Å
R-Value Free:
0.237 (Depositor), 0.263 (DCC)
R-Value Work:
0.210 (Depositor), 0.245 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Mix-and-spray grid preparation for time-resolved MicroED

Summers, J.A., Vlahakis, N.W., Zielinski, K.A., Uttormark, S., Dolamore, C., Antolini, C., Wilson, M.A., Pollack, L., Rodriguez, J.A., Dahlberg, P.D., Wakatsuki, S.

To be published.

Macromolecule Content

Total Structure Weight: 58.08 kDa
Atom Count: 4,092
Modeled Residue Count: 558
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A, B	279	Parengyodontium album	Mutation(s): 1 EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873 Go to UniProtKB: P06873
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06873
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 2.20 Å
R-Value Free: 0.237 (Depositor), 0.263 (DCC)
R-Value Work: 0.210 (Depositor), 0.245 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.3	α = 90
b = 129.1	β = 90.9
c = 47.7	γ = 90

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-01

Deposition Author(s):

Rodriguez, J.A.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-07-01
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.