4HK9

Crystal Structures of Mutant Endo-beta-1,4-xylanase II Complexed with substrate (1.15 A) and Products (1.6 A)

• PDB DOI: https://doi.org/10.2210/pdb4HK9/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-10-15 Released: 2014-01-08 
• Deposition Author(s): Langan, P., Wan, Q., Coates, L., Kovalevsky, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.179 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6JUG 6JWB 6JXL 6K9R

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 21.06 kDa 
• Atom Count: 1,751 
• Modelled Residue Count: 188 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase 2	A	188	Trichoderma reesei	Mutation(s): 1  Gene Names: xyn2 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G87429QT GlyCosmos:  G87429QT

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117	B	4beta-beta-xylotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.179 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.396	α = 90
b = 59.575	β = 90
c = 62.117	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-08 
Deposition Author(s): Langan, P., Wan, Q., Coates, L., Kovalevsky, A.

Revision History  

• Version 1.0: 2014-01-08
  Type: Initial release
  
• Version 1.1: 2014-02-12
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Structure summary