9OZY | pdb_00009ozy

Gradient equilibration of hexagonal thermolysin to low salt over 15 minutes

• PDB DOI: https://doi.org/10.2210/pdb9OZY/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Mutation(s): No 


• Deposited: 2025-06-06 Released: 2025-10-15 
• Deposition Author(s): Juers, D.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Automated gradient equilibration of macromolecular crystals to new solution conditions.

Juers, D.H., Quire, J., Stothers, S.

(2025) Acta Crystallogr F Struct Biol Commun 81: 478-486

• PubMed: 41042616 
• DOI: https://doi.org/10.1107/S2053230X25008398
• Primary Citation of Related Structures:  
  9OZ5, 9OZW, 9OZY


• PubMed Abstract: 
  

  We describe a device and a method for changing the ambient solution of a macromolecular crystal. The approach is gentle, automated, inexpensive and open source. Examples are given of the equilibration of three different crystals to new solutions with exchange times ranging from 5 to 180 min. In each case direct transfer of the crystal to the new solution causes cracking, which is eliminated with gradient equilibration using the described device. Crystals equilibrated with the device produce high-quality diffraction that yields refined structures comparable to those determined previously. The device offers a more systematic and labor-saving workflow than current practice both for performing diffraction analysis of macromolecular crystals and for investigating the response of macromolecular crystals to changes in solution composition.

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Organizational Affiliation: 
• Department of Physics, Whitman College, Walla Walla, WA 99362, USA.

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: 34.93 kDa 
• Atom Count: 2,706 
• Modeled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A [auth E]	316	Geobacillus stearothermophilus	Mutation(s): 0  EC: 3.4.24.27
UniProt
Find proteins for P43133 (Geobacillus stearothermophilus) Explore P43133  Go to UniProtKB:  P43133

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	C [auth E]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL	B [auth E]	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
DMS	I [auth E]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	H [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth E], E, F [auth E], G [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.572	α = 90
b = 93.572	β = 90
c = 131.042	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Juers, D.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM090248

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release
  
• Version 1.1: 2025-11-12
  Changes: Database references