6J43

Proteinase K determined by PAL-XFEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography.

Lee, D.Park, S.Lee, K.Kim, J.Park, G.Nam, K.H.Baek, S.Chung, W.K.Lee, J.L.Cho, Y.Park, J.

(2020) J Appl Crystallogr 53: 477-485

  • DOI: 10.1107/S1600576720002423
  • Primary Citation of Related Structures:  
    6J43

  • PubMed Abstract: 
  • Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented ...

    Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.


    Organizational Affiliation

    PAL-XFEL, Pohang Accelerator Laboratory, 80 Jigok-ro 127 beongil, Pohang, 37673, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteinase KA279Parengyodontium albumMutation(s): 1 
Gene Names: PROK
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.54α = 90
b = 68.54β = 90
c = 108.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-01-07 
  • Released Date: 2020-01-15 
  • Deposition Author(s): Lee, S.J., Park, J.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017M3A9F6029733
National Research Foundation (Korea)Korea, Republic OfNRF-2016R1C1B2014609
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1D1A1B03028119

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references, Derived calculations
  • Version 1.2: 2021-10-20
    Changes: Database references