9FTY | pdb_00009fty

Serial microseconds crystallography at ID29 using fixed-target (small foils): Proteinase K with 20 um spacing between X-ray pulses

• PDB DOI: https://doi.org/10.2210/pdb9FTY/pdb

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


• Deposited: 2024-06-25 Released: 2025-01-22 
• Deposition Author(s): Orlans, J., Rose, S.L., Basu, S., de Sanctis, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.262 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.240 (Depositor) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.

Orlans, J., Rose, S.L., Ferguson, G., Oscarsson, M., Homs Puron, A., Beteva, A., Debionne, S., Theveneau, P., Coquelle, N., Kieffer, J., Busca, P., Sinoir, J., Armijo, V., Lopez Marrero, M., Felisaz, F., Papp, G., Gonzalez, H., Caserotto, H., Dobias, F., Gigmes, J., Lebon, G., Basu, S., de Sanctis, D.

(2025) Commun Chem 8: 6-6

• PubMed: 39775172 
• DOI: https://doi.org/10.1038/s42004-024-01404-y
• Primary Citation Related Structures: 
  9FTS, 9FTU, 9FTV, 9FTX, 9FTY, 9FU1, 9FUD, 9FUE, 9FUP


• PubMed Abstract: 
  

  Serial macromolecular crystallography has become a powerful method to reveal room temperature structures of biological macromolecules and perform time-resolved studies. ID29, a flagship beamline of the ESRF 4th generation synchrotron, is the first synchrotron beamline in the world capable of delivering high brilliance microsecond X-ray pulses at high repetition rate for the structure determination of biological macromolecules at room temperature. The cardinal combination of microsecond exposure times, innovative beam characteristics and adaptable sample environment provides high quality complete data, even from an exceptionally small amount of crystalline material, enabling what we collectively term serial microsecond crystallography (SµX). After validating the use of different sample delivery methods with various model systems, we applied SµX to an integral membrane receptor, where only a few thousands diffraction images were sufficient to obtain a fully interpretable electron density map for the antagonist istradefylline-bound A _2A receptor conformation, providing access to the antagonist binding mode. SµX, as demonstrated at ID29, will quickly find its broad applicability at upcoming 4th generation synchrotron sources worldwide and opens a new frontier in time-resolved SµX.

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Organizational Affiliation: 
• ESRF - The European Synchrotron, 71 Avenue des Martyrs, Grenoble, France.
Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France.
European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France.
European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France. [e-mail].
ESRF - The European Synchrotron, 71 Avenue des Martyrs, Grenoble, France. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.1 kDa 
• Atom Count: 2,168 
• 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
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.262 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.240 (Depositor) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.72	α = 90
b = 68.72	β = 90
c = 108.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Orlans, J., Rose, S.L., Basu, S., de Sanctis, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release