9UPA | pdb_00009upa

Improved thermostability of a GH10 xylanase based on its X-ray crystal structure

• PDB DOI: https://doi.org/10.2210/pdb9UPA/pdb

• Classification: CARBOHYDRATE
• Organism(s): Massilia sp. RBM26
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-28 Released: 2025-06-11 
• Deposition Author(s): Dong, P.P., Lu, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.295 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.241 (DCC) 

Starting Model: experimental

Literature

Improved thermostability of a GH10 xylanase based on its X-ray crystal structure

Dong, P.P., Lu, P.

To be published.

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: 78.98 kDa 
• Atom Count: 5,629 
• Modeled Residue Count: 706 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	353	Massilia sp. RBM26	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for A0A0S2I9J6 (Massilia sp. RBM26) Explore A0A0S2I9J6  Go to UniProtKB:  A0A0S2I9J6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.295 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.241 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.35	α = 90
b = 69.3	β = 91.914
c = 91.08	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Dong, P.P., Lu, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--
Other government	China	Zhejiang Provincial Natural Science Foundation of China LQN25C050002

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release