6RV9

Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor inactive S270A variant in complex with the aldouronic acid XUXXR

• PDB DOI: https://doi.org/10.2210/pdb6RV9/pdb

• Classification: HYDROLASE
• Organism(s): Cerrena unicolor
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2019-05-31 Released: 2020-03-18 
• Deposition Author(s): Ernst, H.A., Mosbech, C., Langkilde, A., Westh, P., Meyer, A., Agger, J.W., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.66 kDa 
• Atom Count: 6,347 
• Modelled Residue Count: 760 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-O-methyl-glucuronoyl methylesterase	A, B	401	Cerrena unicolor	Mutation(s): 1  EC: 3.1.1
UniProt
Find proteins for A0A0A7EQR3 (Cerrena unicolor) Explore A0A0A7EQR3  Go to UniProtKB:  A0A0A7EQR3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-Xylitol	C	5		N/A
Glycosylation Resources
GlyTouCan:  G92772TT GlyCosmos:  G92772TT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.481	α = 90
b = 84.481	β = 90
c = 261.732	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Ernst, H.A., Mosbech, C., Langkilde, A., Westh, P., Meyer, A., Agger, J.W., Larsen, S.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary