Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 76.69 kDa 
• Atom Count: 5985 
• Modelled Residue Count: 667 
• Deposited Residue Count: 670 
• Unique protein chains: 1

5XZU

Crystal structure of GH10 xylanase from Bispora. sp MEY-1 with xylobiose

• DOI: 10.2210/pdb5XZU/pdb

• Classification: HYDROLASE
• Organism(s): Bispora sp. MEY-1
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2017-07-14 Released: 2018-05-02 
• Deposition Author(s): You, S., Chen, C.C., Tu, T., Guo, R.T., Luo, H.Y., Yao, B.
• Funding Organization(s): the National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.183 
• R-Value Work: 0.124 
• R-Value Observed: 0.127 

Literature

Insight into the functional roles of Glu175 in the hyperthermostable xylanase XYL10C-Delta N through structural analysis and site-saturation mutagenesis.

You, S., Chen, C.C., Tu, T., Wang, X., Ma, R., Cai, H.Y., Guo, R.T., Luo, H.Y., Yao, B.

(2018) Biotechnol Biofuels 11: 159-159

• PubMed: 29930705 
• DOI: 10.1186/s13068-018-1150-8
• Primary Citation of Related Structures:  
  5XZU


• PubMed Abstract: 
  

Improving the hydrolytic performance of hemicellulases to degrade lignocellulosic biomass is of considerable importance for second-generation biorefinery. Xylanase, as the crucial hemicellulase, must be thermostable and have high activity for its potential use in the bioethanol industry. To obtain excellent xylanase candidates, it is necessary to understand the structure-function relationships to provide a meaningful reference to improve the enzyme properties. This study aimed to investigate the catalytic mechanism of a highly active hyperthermophilic xylanase variant, XYL10C-ΔN, for hemicellulose degradation.

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Organizational Affiliation: 

1Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	335	Bispora sp. MEY-1	Mutation(s): 0  Gene Names: xyl10C EC: 3.2.1.8
UniProt
Find proteins for D0QF43 (Bispora sp. MEY-1) Explore D0QF43  Go to UniProtKB:  D0QF43

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	C	beta-cellobiose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.183 
• R-Value Work: 0.124 
• R-Value Observed: 0.127 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.274	α = 90
b = 83.136	β = 94.25
c = 65.387	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-07-14 
• Released Date: 2018-05-02 
Deposition Author(s): You, S., Chen, C.C., Tu, T., Guo, R.T., Luo, H.Y., Yao, B.

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Funding Organization	Location	Grant Number
the National Natural Science Foundation of China	China	31472127

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary