5A7E | pdb_00005a7e

Crystallographic Structural Determination of a Trigonal Laccase from Coriolopsis Gallica (CgL) to 1.5 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5A7E/pdb

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


• Deposited: 2015-07-03 Released: 2016-05-25 
• Deposition Author(s): Ruiz-Arellano, R.R., Diaz, A., Ayala, M., De la Mora, E., Rudino-Pinera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Metal Site Delocalization Observed in a Model Multicopper Oxidase: An Insight Into Water Release Mechanism

De la Mora, E., Morales, N., Rodriguez-Almazan, G., Ruiz-Arellano, R.R., Rudino-Pinira, E.

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: 55.06 kDa 
• Atom Count: 4,646 
• Modeled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CORIOLOPSIS GALLICA LACCASE	A	496	Coriolopsis gallica	Mutation(s): 0  EC: 1.10.3.2
UniProt
Find proteins for Q1W6B1 (Coriolopsis gallica) Explore Q1W6B1  Go to UniProtKB:  Q1W6B1
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3	N/A	N-Glycosylation

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(3-3)-[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	C	5	N/A	N-Glycosylation

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-2)-beta-D-glucopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan: G26080VZ GlyCosmos: G26080VZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	E [auth A], F [auth A], G [auth A], H [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.742	α = 75.67
b = 56.406	β = 73.03
c = 59.173	γ = 76.49

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Ruiz-Arellano, R.R., Diaz, A., Ayala, M., De la Mora, E., Rudino-Pinera, E.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 3.0: 2021-04-28
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2022-12-07
  Changes: Data collection, Database references
• Version 4.0: 2023-01-18
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 4.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 4.2: 2024-11-20
  Changes: Structure summary