2HIS | pdb_00002his

CELLULOMONAS FIMI XYLANASE/CELLULASE DOUBLE MUTANT E127A/H205N WITH COVALENT CELLOBIOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.280 (Depositor) 
  • R-Value Work: 
    0.220 (Depositor) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.3 of the entry. See complete history

Literature

Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants.

Notenboom, V.Birsan, C.Nitz, M.Rose, D.R.Warren, R.A.Withers, S.G.

(1998) Nat Struct Biol 5: 812-818

  • DOI: https://doi.org/10.1038/1852
  • Primary Citation Related Structures: 
    2HIS

  • PubMed Abstract: 

    The catalytic mechanism of 'retaining' beta-glycosidases has been the subject of considerable interest and debate for many years. The visualization of a covalent glycosyl enzyme intermediate by X-ray crystallography was first accomplished with a saccharide substrate substituted with fluorine at its 2-position. The structure implicated major roles for residue His 205 and for the 2-hydroxyl position of the proximal saccharide in binding and catalysis. Here we have studied the kinetic behavior of various His 205 mutants. One of these mutants, a double mutant H205N/E127A, has been used to stabilize a covalent glycosyl-enzyme intermediate involving an unsubstituted sugar, permitting crystallographic analysis of the interactions between its 2-hydroxyl group and the enzyme.


  • Organizational Affiliation
    • Protein Engineering Network of Centres of Excellence, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Canada.

Macromolecule Content 

  • Total Structure Weight: 34.31 kDa 
  • Atom Count: 2,543 
  • Modeled Residue Count: 312 
  • Deposited Residue Count: 312 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CELLULOMONAS FIMI FAMILY 10 BETA-1,4-GLYCANASE312Cellulomonas fimiMutation(s): 2 
EC: 3.2.1.91 (PDB Primary Data), 3.2.1.8 (UniProt)
UniProt
Find proteins for P07986 (Cellulomonas fimi)
Explore P07986 
Go to UniProtKB:  P07986
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07986
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G86802XL
GlyCosmos: G86802XL

Biologically Interesting Molecules (External Reference) 

1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_900023
Query on PRD_900023
B
alpha-cellobioseOligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.280 (Depositor) 
  • R-Value Work:  0.220 (Depositor) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.411α = 90
b = 88.411β = 90
c = 80.675γ = 90
Software Package:
Software NamePurpose
SDMWdata collection
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
XENGENdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-09
    Changes: Refinement description
  • Version 2.3: 2024-10-16
    Changes: Data collection, Structure summary