5LDU | pdb_00005ldu

Recombinant high-redox potential laccase from Basidiomycete Trametes hirsuta

• PDB DOI: https://doi.org/10.2210/pdb5LDU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trametes hirsuta
• Expression System: Penicillium canescens
• Mutation(s): No 


• Deposited: 2016-06-27 Released: 2016-08-10 
• Deposition Author(s): Polyakov, K.M., Fedorova, T.V., Loginov, D.S., Savinova, O.S., Lamzin, V.S., Koroleva, O.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

First structure of recombinant high-redox potential laccase from Basidiomycete Trametes hirsuta.

Fedorova, T.V., Polyakov, K.M., Loginov, D.S., Savinova, O.S., Vavilova, E.A., Chulkin, A.M., Lamzin, V.S., Koroleva, O.V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.27 kDa 
• Atom Count: 4,238 
• Modeled Residue Count: 499 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase A	A	499	Trametes hirsuta	Mutation(s): 0  EC: 1.10.3.2
UniProt
Find proteins for A0A0A7M685 (Trametes hirsuta) Explore A0A0A7M685  Go to UniProtKB:  A0A0A7M685
Glycosylation
Glycosylation Sites: 5

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[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-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth A], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	D [auth A], E [auth A], F [auth A], G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NA	L [auth A], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.65	α = 90
b = 160.65	β = 90
c = 53.46	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Polyakov, K.M., Fedorova, T.V., Loginov, D.S., Savinova, O.S., Lamzin, V.S., Koroleva, O.V.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary