6QXV | pdb_00006qxv

Pink beam serial crystallography: Proteinase K, 1 us exposure, 1585 patterns merged (2 chips)

• PDB DOI: https://doi.org/10.2210/pdb6QXV/pdb

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


• Deposited: 2019-03-08 Released: 2019-09-25 
• Deposition Author(s): Tolstikova, A., Oberthuer, D., Meents, A.
• Funding Organization(s): European Commission, German Federal Ministry for Education and Research, European Research Council, European Union

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector.

Tolstikova, A., Levantino, M., Yefanov, O., Hennicke, V., Fischer, P., Meyer, J., Mozzanica, A., Redford, S., Crosas, E., Opara, N.L., Barthelmess, M., Lieske, J., Oberthuer, D., Wator, E., Mohacsi, I., Wulff, M., Schmitt, B., Chapman, H.N., Meents, A.

(2019) IUCrJ 6: 927-937

• PubMed: 31576225 
• DOI: https://doi.org/10.1107/S205225251900914X
• Primary Citation Related Structures: 
  6QXV, 6QXW, 6QXX, 6QXY, 6QY0, 6QY1, 6QY2, 6QY4, 6QY5


• PubMed Abstract: 
  

  Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.

---

Organizational Affiliation: 
• Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.
Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany.
Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland.
C-CINA, Biozentrum, University of Basel, Mattenstrasse 26, 4002 Basel, Switzerland.
Malopolska Centre of Biotechnology, Jagiellonian University, Cracow 30-387, Poland.
Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany.

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: 30.2 kDa 
• Atom Count: 2,493 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	O [auth A], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.62	α = 90
b = 68.62	β = 90
c = 104.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Tolstikova, A., Oberthuer, D., Meents, A.

---

Funding Organization	Location	Grant Number
European Commission		637295
German Federal Ministry for Education and Research	Germany	031B0405D
European Research Council		609920
European Union		654220
German Federal Ministry for Education and Research	Germany	05K2018 - 2017-06727

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary