3KW8

Two-domain laccase from Streptomyces coelicolor at 2.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KW8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces coelicolor
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2009-12-01 Released: 2010-12-08 
• Deposition Author(s): Skalova, T., Dohnalek, J., Kolenko, P., Duskova, J., Stepankova, A., Hasek, J., Ostergaard, L.H., Ostergaard, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.178 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Literature

Structure of laccase from Streptomyces coelicolor after soaking with potassium hexacyanoferrate and at an improved resolution of 2.3 A

Skalova, T., Duskova, J., Hasek, J., Stepankova, A., Koval, T., Ostergaard, L.H., Dohnalek, J.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 27-32

• PubMed: 21206017 
• DOI: https://doi.org/10.1107/S1744309110046099
• Primary Citation of Related Structures:  
  3KW8


• PubMed Abstract: 
  

  The paper reports the structure of the small laccase from Streptomyces coelicolor determined from a crystal soaked with potassium hexacyanoferrate [K4Fe(CN)6]. The decolorization of the natively blue crystal observed upon soaking indicates the reduction of the enzyme in the crystal. The ligand binds between laccase molecules and stabilizes the crystal. The increased diffraction limit of the diffraction data collected from this crystal enabled the refinement of the small laccase structure at 2.3 Å resolution, which is the highest resolution obtained to date.

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Organizational Affiliation: 

Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.57 kDa 
• Atom Count: 2,430 
• Modelled Residue Count: 273 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative copper oxidase	A	276	Streptomyces coelicolor	Mutation(s): 0  Gene Names: SC4C6.22 EC: 1.10.3.2
UniProt
Find proteins for Q9XAL8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9XAL8  Go to UniProtKB:  Q9XAL8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	I [auth A], M [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	J [auth A], K [auth A], L [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CU	B [auth A], C [auth A], D [auth A], E [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
FE	F [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.178 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 4₃ 3 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/717

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.723	α = 90
b = 176.723	β = 90
c = 176.723	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Skalova, T., Dohnalek, J., Kolenko, P., Duskova, J., Stepankova, A., Hasek, J., Ostergaard, L.H., Ostergaard, P.R.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-02
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description