5FSJ

Structure of thermolysin prepared by the 'soak-and-freeze' method under 45 bar of oxygen pressure

• PDB DOI: https://doi.org/10.2210/pdb5FSJ/pdb

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


• Deposited: 2016-01-06 Released: 2016-10-26 
• Deposition Author(s): Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.122 
• R-Value Work: 0.104 
• R-Value Observed: 0.105 

Starting Model: experimental

Literature

Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology.

Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

(2016) J Appl Crystallogr 49: 1478

• DOI: https://doi.org/10.1107/S1600576716010992

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: 34.99 kDa 
• Atom Count: 3,155 
• 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  EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	C [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL	B [auth A]	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
ZN	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A], J [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
OXY	I [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.122 
• R-Value Work: 0.104 
• R-Value Observed: 0.105 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.922	α = 90
b = 92.922	β = 90
c = 130.252	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Structure summary
• Version 1.2: 2018-02-21
  Changes: Advisory, Database references, Structure summary
• Version 2.0: 2018-06-20
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description