6IG7

Crystal structure of thermolysin delivered in polyacrylamide using x-ray free electron laser

• PDB DOI:  https://doi.org/10.2210/pdb6IG7/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thermoproteolyticus
• Expression System: Bacillus thermoproteolyticus
• Mutation(s): No 


• Deposited: 2018-09-25 Released: 2018-11-07 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 

Literature

Polyacrylamide injection matrix for serial femtosecond crystallography.

Park, J., Park, S., Kim, J., Park, G., Cho, Y., Nam, K.H.

(2019) Sci Rep 9: 2525-2525

• PubMed: 30792457 
• DOI: https://doi.org/10.1038/s41598-019-39020-9
• Primary Citation of Related Structures:  
  6IG6, 6IG7


• PubMed Abstract: 
  

Serial femtosecond crystallography (SFX) provides opportunities to observe the dynamics of macromolecules without causing radiation damage at room temperature. Although SFX provides a biologically more reliable crystal structure than provided by the existing synchrotron sources, there are limitations due to the consumption of many crystal samples. A viscous medium as a carrier matrix reduces the flow rate of the crystal sample from the injector, thereby dramatically reducing sample consumption. However, the currently available media cannot be applied to specific crystal samples owing to reactions between the viscous medium and crystal sample. The discovery and characterisation of a new delivery medium for SFX can further expand its use. Herein, we report the preparation of a polyacrylamide (PAM) injection matrix to determine the crystal structure with an X-ray free-electron laser. We obtained 11,936 and 22,213 indexed images using 0.5 mg lysozyme and 1.0 mg thermolysin, respectively. We determined the crystal structures of lysozyme and thermolysin delivered in PAM at 1.7 Å and 1.8 Å resolutions. The maximum background scattering from PAM was lower than monoolein, a commonly used viscous medium. Our results show that PAM can be used as a sample delivery media in SFX studies.

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Organizational Affiliation: 

Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. [e-mail].

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: 34.86 kDa 
• Atom Count: 2,603 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	316	Bacillus thermoproteolyticus	Mutation(s): 0  Gene Names: npr EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	H [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
LEU	G [auth A]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.11577/1502065
• Diffraction Data: https://doi.org/10.11577/1469473

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.663	α = 90
b = 92.663	β = 90
c = 128.591	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 2.0: 2019-01-23
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2019-05-22
  Changes: Data collection, Database references
• Version 2.2: 2019-08-28
  Changes: Data collection
• Version 2.3: 2019-09-18
  Changes: Data collection
• Version 2.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations