1BS9 | pdb_00001bs9

ACETYLXYLAN ESTERASE FROM P. PURPUROGENUM REFINED AT 1.10 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.182 (Depositor) 
  • R-Value Observed: 
    0.128 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1BS9

This is version 1.3 of the entry. See complete history

Literature

Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase.

Ghosh, D.Erman, M.Sawicki, M.Lala, P.Weeks, D.R.Li, N.Pangborn, W.Thiel, D.J.Jornvall, H.Gutierrez, R.Eyzaguirre, J.

(1999) Acta Crystallogr D Biol Crystallogr 55: 779-784

  • DOI: https://doi.org/10.1107/s0907444999000244
  • Primary Citation Related Structures: 
    1BS9, 2AXE

  • PubMed Abstract: 

    Enzymatic and non-enzymatic iodination of the amino acid tyrosine is a well known phenomenon. The iodination technique has been widely used for labeling proteins. Using high-resolution X-ray crystallographic techniques, the chemical and three-dimensional structures of iodotyrosines formed by non-enzymatic incorporation of I atoms into tyrosine residues of a crystalline protein are described. Acetylxylan esterase (AXE II; 207 amino-acid residues) from Penicillium purpurogenum has substrate specificities towards acetate esters of D-xylopyranose residues in xylan and belongs to a new class of alpha/beta hydrolases. The crystals of the enzyme are highly ordered, tightly packed and diffract to better than sub-angström resolution at 85 K. The iodination technique has been utilized to prepare an isomorphous derivative of the AXE II crystal. The structure of the enzyme determined at 1.10 A resolution exclusively by normal and anomalous scattering from I atoms, along with the structure of the iodinated complex at 1.80 A resolution, demonstrate the formation of covalent bonds between I atoms and C atoms at ortho positions to the hydroxyl groups of two tyrosyl moieties, yielding iodotyrosines.


  • Organizational Affiliation
    • Hauptman-Woodward Medical Research Institute, 73 High Street, Buffalo, New York 14203, USA. ghosh@hwi.buffalo.edu

Macromolecule Content 

  • Total Structure Weight: 20.76 kDa 
  • Atom Count: 1,598 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 207 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYL XYLAN ESTERASE207Talaromyces purpureogenusMutation(s): 0 
EC: 3.1.1.6 (PDB Primary Data), 3.1.1.72 (UniProt)
UniProt
Find proteins for O59893 (Talaromyces purpureogenus)
Explore O59893 
Go to UniProtKB:  O59893
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59893
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.182 (Depositor) 
  • R-Value Observed: 0.128 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.886α = 90
b = 60.983β = 90
c = 72.425γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXmodel building
SHELXrefinement
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary