3ZDW

Substrate and dioxygen binding to the endospore coat laccase CotA from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3ZDW/pdb
• Entry: 3ZDW supersedes: 1UVW

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-12-01 Released: 2012-12-19 
• Deposition Author(s): Enguita, F.J., Marcal, D., Grenha, R., Lindley, P.F., Carrondo, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Substrate and Dioxygen Binding to the Endospore Coat Laccase from Bacillus Subtilis.

Enguita, F.J., Marcal, D., Martins, L.O., Grenha, R., Henriques, A.O., Lindley, P.F., Carrondo, M.A.

(2004) J Biol Chem 279: 23472

• PubMed: 14764581 
• DOI: https://doi.org/10.1074/jbc.M314000200
• Primary Citation of Related Structures:  
  3ZDW


• PubMed Abstract: 
  

  The CotA laccase from the endospore coat of Bacillus subtilis has been crystallized in the presence of the non-catalytic co-oxidant 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS), and the structure was determined using synchrotron radiation. The binding site for this adduct is well defined and indicates how ABTS, in conjunction with laccases, could act as an oxidative mediator toward non-phenolic moieties. In addition, a dioxygen moiety is clearly defined within the solvent channel oriented toward one of the T3 copper atoms in the trinuclear center.

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Organizational Affiliation: 

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.

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: 60.02 kDa 
• Atom Count: 4,294 
• Modelled Residue Count: 503 
• Deposited Residue Count: 513 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COTA LACCASE	A	513	Bacillus subtilis	Mutation(s): 0  EC: 1.10.3.2 (UniProt), 1.3.3.5 (UniProt)
UniProt
Find proteins for P07788 (Bacillus subtilis (strain 168)) Explore P07788  Go to UniProtKB:  P07788

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EBS	G [auth A]	3-ETHYL-2-[(2Z)-2-(3-ETHYL-6-SULFO-1,3-BENZOTHIAZOL-2(3H)-YLIDENE)HYDRAZINO]-6-SULFO-3H-1,3-BENZOTHIAZOL-1-IUM C18 H18 N4 O6 S4 ZTOJFFHGPLIVKC-YAFCTCPESA-N
GOL	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU1	B [auth A], C [auth A], D [auth A], E [auth A]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
OXY	F [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.14	α = 90
b = 102.14	β = 90
c = 136.85	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Enguita, F.J., Marcal, D., Grenha, R., Lindley, P.F., Carrondo, M.A.
• This entry supersedes: 1UVW

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary