5GQD | pdb_00005gqd

Crystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86

• PDB DOI: https://doi.org/10.2210/pdb5GQD/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: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.79 kDa 
• Atom Count: 7,547 
• Modeled Residue Count: 854 
• 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
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G73335RX GlyCosmos: G73335RX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.186	α = 90
b = 94.045	β = 90
c = 140.078	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: 2024-11-20
  Changes: Structure summary