1J01 | pdb_00001j01

Crystal Structure Of The Xylanase Cex With Xylobiose-Derived Inhibitor Isofagomine lactam

• PDB DOI: https://doi.org/10.2210/pdb1J01/pdb

• Classification: HYDROLASE
• Organism(s): Cellulomonas fimi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-10-25 Released: 2002-11-06 
• Deposition Author(s): Williams, S.J., Notenboom, V., Wicki, J., Rose, D.R., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

A New, Simple, High-Affinity Glycosidase Inhibitor: Analysis of Binding through X-ray Crystallography, Mutagenesis, and Kinetic Analysis

Williams, S.J., Notenboom, V., Wicki, J., Rose, D.R., Withers, S.G.

(2000) J Am Chem Soc 122: 4229-4230

• DOI: https://doi.org/10.1021/ja0002870

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.32 kDa 
• Atom Count: 2,578 
• Modeled Residue Count: 312 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-1,4-xylanase	A	312	Cellulomonas fimi	Mutation(s): 0  Gene Names: Cex 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XIL	B [auth A]	(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside C10 H17 N O7 BHZMHPRIYUPDCT-BQWZOORQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.209 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.996	α = 90
b = 86.996	β = 90
c = 80.364	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-06 
Deposition Author(s): Williams, S.J., Notenboom, V., Wicki, J., Rose, D.R., Withers, S.G.

Revision History  

• Version 1.0: 2002-11-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Derived calculations, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary