5MIG

The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The 16-th structure of the series with total exposition time 453 min. The crystal was quick refreezing before this data collection.

• PDB DOI: https://doi.org/10.2210/pdb5MIG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Steccherinum murashkinskyi
• Mutation(s): No 


• Deposited: 2016-11-28 Released: 2017-05-10 
• Deposition Author(s): Polyakov, K.M., Gavryushov, S., Fedorova, T.V., Glazunova, O.A., Popov, A.N.
• Funding Organization(s): RFBR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.162 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.9 kDa 
• Atom Count: 4,660 
• Modelled Residue Count: 499 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase 2	A	546	Steccherinum murashkinskyi	Mutation(s): 0  EC: 1.10.3.2
UniProt
Find proteins for I1VE66 (Steccherinum murashkinskyi) Explore I1VE66  Go to UniProtKB:  I1VE66

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	H [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CU	D [auth A], E [auth A], F [auth A], G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.162 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.268	α = 90
b = 84.415	β = 90
c = 112.384	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Polyakov, K.M., Gavryushov, S., Fedorova, T.V., Glazunova, O.A., Popov, A.N.

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Funding Organization	Location	Grant Number
RFBR	Russian Federation	16-04-0052

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary