3ZI6

Structure of thermolysin solved by SAD from data collected by Direct Data Collection (DDC) using the GRob robot goniometer

• PDB DOI: https://doi.org/10.2210/pdb3ZI6/pdb

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


• Deposited: 2013-01-04 Released: 2013-05-01 
• Deposition Author(s): Bowler, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Recent Progress in Robot-Based Systems for Crystallography and Their Contribution to Drug Discovery.

Ferrer, J.L., Larive, N.A., Bowler, M.W., Nurizzo, D.

(2013) Expert Opin Drug Discov 8: 835

• PubMed: 23656378 
• DOI: https://doi.org/10.1517/17460441.2013.793666
• Primary Citation of Related Structures:  
  3ZI6, 3ZI7


• PubMed Abstract: 
  

  X-ray crystallography is the main tool for macromolecular structure solution at atomic resolution. It provides key information for the understanding of protein function, opening opportunities for the modulation of enzymatic mechanisms, and protein-ligand interactions. As a consequence, macromolecular crystallography plays an essential role in drug design, as well as in the a posteriori validation of drug mechanisms.

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Organizational Affiliation: 

Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier (UJF), Institut de Biologie Structurale Jean-Pierre Ebel (IBS), F-38027 Grenoble Cedex 1, France. [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: 34.85 kDa 
• Atom Count: 2,662 
• 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 4 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	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.754	α = 90
b = 92.754	β = 90
c = 129.224	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELXCDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Bowler, M.W.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references, Refinement description, Structure summary
• Version 1.2: 2013-07-03
  Changes: Database references
• Version 1.3: 2018-06-20
  Changes: Advisory, Data collection, Derived calculations