5GQE

Crystal structure of michaelis complex of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86

• PDB DOI: https://doi.org/10.2210/pdb5GQE/pdb

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


• Deposited: 2016-08-07 Released: 2017-08-09 
• Deposition Author(s): Suzuki, R., Fujimoto, Z., Kaneko, S., Kuno, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant

Suzuki, R., Fujimoto, Z., Kaneko, S., Hasegawa, T., Kuno, A.

(2019) J Appl Glycosci (1999) 65

• DOI: https://doi.org/10.5458/jag.jag.JAG-2017_011

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.37 kDa 
• Atom Count: 7,400 
• Modelled Residue Count: 858 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	436	Streptomyces olivaceoviridis	Mutation(s): 3  EC: 3.2.1.8
UniProt
Find proteins for Q7SI98 (Streptomyces olivaceoviridis) Explore Q7SI98  Go to UniProtKB:  Q7SI98

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-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, F	5		N/A
Glycosylation Resources
GlyTouCan:  G47101GE GlyCosmos:  G47101GE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	D	4		N/A
Glycosylation Resources
GlyTouCan:  G60650FG GlyCosmos:  G60650FG

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	E, G	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	H	3		N/A
Glycosylation Resources
GlyTouCan:  G87429QT GlyCosmos:  G87429QT

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	E, G	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117	H	4beta-beta-xylotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.13	α = 90
b = 94.007	β = 90
c = 137.641	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Suzuki, R., Fujimoto, Z., Kaneko, S., Kuno, A.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary