2HRG | pdb_00002hrg

Crystal Structure of Blue Laccase from Trametes trogii complexed with p-methylbenzoate

• PDB DOI: https://doi.org/10.2210/pdb2HRG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Coriolopsis trogii
• Mutation(s): No 


• Deposited: 2006-07-20 Released: 2007-09-11 
• Deposition Author(s): Matera, I., Gullotto, A., Ferraroni, M., Tilli, S., Briganti, F., Scozzafava, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the blue multicopper oxidase from the white-rot fungus Trametes trogii complexed with p-toluate

Matera, I., Gullotto, A., Tilli, S., Ferraroni, M., Scozzafava, A., Briganti, F.

(2008) Inorganica Chim Acta 361: 4129-4137

• DOI: https://doi.org/10.1016/j.ica.2008.03.091

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: 55.1 kDa 
• Atom Count: 4,476 
• Modeled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase	A	496	Coriolopsis trogii	Mutation(s): 0  EC: 1.10.3.2
UniProt
Find proteins for Q9HDQ0 (Coriolopsis trogii) Explore Q9HDQ0  Go to UniProtKB:  Q9HDQ0
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4MA	N [auth A]	4-METHYLBENZOIC ACID C8 H8 O2 LPNBBFKOUUSUDB-UHFFFAOYSA-N
GOL	K [auth A], L [auth A], M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	G [auth A], H [auth A], I [auth A], J [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	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: 1.58 Å
• R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.385	α = 90
b = 85.128	β = 90
c = 108.561	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Matera, I., Gullotto, A., Ferraroni, M., Tilli, S., Briganti, F., Scozzafava, A.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary