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 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