1OD8

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam

• PDB DOI: https://doi.org/10.2210/pdb1OD8/pdb

• Classification: HYDROLASE/LECTIN
• Organism(s): Streptomyces lividans
• Expression System: Streptomyces lividans
• Mutation(s): No 


• Deposited: 2003-02-14 Released: 2003-04-08 
• Deposition Author(s): Gloster, T.M., Roberts, S., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.126 
• R-Value Work: 0.103 
• R-Value Observed: 0.104 

Starting Model: experimental

Literature

A Xylobiose-Derived Isofagomine Lactam Glycosidase Inhibitor Binds as its Amide Tautomer

Gloster, T.M., Williams, S.J., Tarling, C., Roberts, S., Dupont, C., Jodoin, P., Shareck, F., Withers, S.G., Davies, G.J.

(2003) Chem Commun (Camb) 8: 944

• PubMed: 12744311 
• DOI: https://doi.org/10.1039/b301829f
• Primary Citation of Related Structures:  
  1OD8


• PubMed Abstract: 
  

  The atomic-resolution structure of a xylobiose-derived isofagomine lactam in complex with the xylanase Xyn10A from Streptomyces lividans reveals that the lactam is bound to the enzyme as the amide tautomer, with "reversed" protonation-states for nucleophile and acid-base.

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Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.89 kDa 
• Atom Count: 3,076 
• Modelled Residue Count: 302 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE A	A	313	Streptomyces lividans	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for P26514 (Streptomyces lividans) Explore P26514  Go to UniProtKB:  P26514

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	F [auth A], J [auth A]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
XDL	E [auth A], I [auth A]	XYLOSE-DERIVED ISOFAGOMINE LACTAM C5 H9 N O2 RYKLZUPYJFFNRR-BYPYZUCNSA-N
IMD	G [auth A], H [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
NA	B [auth A], C [auth A], D [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.126 
• R-Value Work: 0.103 
• R-Value Observed: 0.104 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.814	α = 90
b = 45.878	β = 90
c = 85.737	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-08 
Deposition Author(s): Gloster, T.M., Roberts, S., Davies, G.J.

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  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, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary