6GRW

Glucuronoyl Esterase from Opitutus terrae (Au derivative)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion.

Arnling Baath, J.Mazurkewich, S.Knudsen, R.M.Poulsen, J.N.Olsson, L.Lo Leggio, L.Larsbrink, J.

(2018) Biotechnol Biofuels 11: 213-213

  • DOI: https://doi.org/10.1186/s13068-018-1213-x
  • Primary Citation of Related Structures:  
    6GRW, 6GRY, 6GS0, 6GU8

  • PubMed Abstract: 

    Lignocellulose is highly recalcitrant to enzymatic deconstruction, where the recalcitrance primarily results from chemical linkages between lignin and carbohydrates. Glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15) have been suggested to play key roles in reducing lignocellulose recalcitrance by cleaving covalent ester bonds found between lignin and glucuronoxylan. However, only a limited number of GEs have been biochemically characterized and structurally determined to date, limiting our understanding of these enzymes and their potential exploration.


  • Organizational Affiliation

    2Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative acetyl xylan esterase403Opitutus terrae PB90-1Mutation(s): 0 
Gene Names: Oter_0116
UniProt
Find proteins for B1ZMF4 (Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1))
Explore B1ZMF4 
Go to UniProtKB:  B1ZMF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1ZMF4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AU
Query on AU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.693α = 76.573
b = 44.608β = 67.172
c = 50.558γ = 70.648
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHENIXphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DenmarkNovo Nordisk Foundation NNF17OC0027698
European UnionDenmarkInterreg-programmet for Oresund-Kattegat-Skagerrak

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release