1REF | pdb_00001ref

ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 2,3-EPOXYPROPYL-BETA-D-XYLOSIDE

• PDB DOI: https://doi.org/10.2210/pdb1REF/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Mutation(s): No 


• Deposited: 1995-12-21 Released: 1997-01-11 
• Deposition Author(s): Rouvinen, J., Havukainen, R., Torronen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.

Havukainen, R., Torronen, A., Laitinen, T., Rouvinen, J.

(1996) Biochemistry 35: 9617-9624

• PubMed: 8755744 
• DOI: https://doi.org/10.1021/bi953052n
• Primary Citation Related Structures: 
  1RED, 1REE, 1REF


• PubMed Abstract: 
  

  The three-dimensional structures of endo-1,4-xylanase II (XYNII) from Trichoderma reesei complexed with 4,5-epoxypentyl beta-D-xyloside (X-O-C5),3,4-epoxybutyl beta-D-xyloside (X-O-C4), and 2,3-epoxypropyl beta-D-xyloside (X-O-C3) were determined by X-ray crystallography. High-resolution measurement revealed clear electron densities for each ligand. Both X-O-C5 and X-O-C3 were found to form a covalent bond with the putative nucleophile Glu86. Unexpectedly, X-O-C4 was found to bind to the putative acid/base catalyst Glu177. In all three complexes, clear conformational changes were found in XYNII compared to the native structure. These changes were largest in the X-O-C3 complex structure.

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Organizational Affiliation: 
• Department of Chemistry, University of Joensuu, Finland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.01 kDa 
• Atom Count: 3,233 
• Modeled Residue Count: 380 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE II	A, B	190	Trichoderma reesei	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for P36217 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30)) Explore P36217  Go to UniProtKB:  P36217

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C3X	D [auth B]	(2R)-oxiran-2-ylmethyl beta-D-xylopyranoside C8 H14 O6 JKWGJZWJCPSTJC-JAJWTYFOSA-N
BEZ	C [auth B]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.34	α = 90
b = 60.88	β = 94.28
c = 37.89	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-01-11 
Deposition Author(s): Rouvinen, J., Havukainen, R., Torronen, A.

Revision History  

• Version 1.0: 1997-01-11
  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: 2019-12-25
  Changes: Derived calculations, Other, Polymer sequence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 2.2: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary