5XZO | pdb_00005xzo

Crystal structure of GH10 xylanase XYL10C from Bispora. sp MEY-1

• PDB DOI: https://doi.org/10.2210/pdb5XZO/pdb

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


• Deposited: 2017-07-13 Released: 2018-01-17 
• Deposition Author(s): You, S., Chen, C., Tu, T., Guo, R.T., Luo, H., Yao, B.
• Funding Organization(s): the National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of GH10 xylanase XYL10C from Bispora. sp MEY-1

You, S., Chen, C., Tu, T.

To be published.

Biological Assembly 1  

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: 76.35 kDa 
• Atom Count: 6,138 
• Modeled Residue Count: 668 
• Deposited Residue Count: 670 
• Unique protein chains: 1

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
Glycosylation
Glycosylation Sites: 2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.457	α = 90
b = 83.262	β = 94.49
c = 65.279	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): You, S., Chen, C., Tu, T., Guo, R.T., Luo, H., 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: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary