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

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
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This is version 1.0 of the entry. See complete history.

Literature

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

Dong, P.P., Lu, P.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S2I9J6
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.