3EIM | pdb_00003eim

Metal exchange in Thermolysin

• PDB DOI: https://doi.org/10.2210/pdb3EIM/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thermoproteolyticus
• Mutation(s): Yes 


• Deposited: 2008-09-16 Released: 2009-10-06 
• Deposition Author(s): Englert, L., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.252 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Metal exchange in Thermolysin

Englert, L., Heine, A., Klebe, G.

To be published.

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: 34.68 kDa 
• Atom Count: 2,656 
• 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	316	Bacillus thermoproteolyticus	Mutation(s): 2  EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU1	B [auth A]	COPPER (I) ION Cu VMQMZMRVKUZKQL-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: 1.88 Å
• R-Value Free:  0.252 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.71	α = 90
b = 92.71	β = 90
c = 128.65	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Englert, L., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description