6JDT | pdb_00006jdt

Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5

• PDB DOI: https://doi.org/10.2210/pdb6JDT/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus fumigatus Z5
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2019-02-02 Released: 2020-05-20 
• Deposition Author(s): Li, G., Miao, Y., Zhang, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.168 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5

Li, G., Miao, Y., Zhang, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.34 kDa 
• Atom Count: 5,414 
• Modeled Residue Count: 638 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	319	Aspergillus fumigatus Z5	Mutation(s): 0  Gene Names: Y699_04481 EC: 3.2.1.8
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.168 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.606	α = 73.86
b = 57.575	β = 80.39
c = 65.088	γ = 68.35

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Li, G., Miao, Y., Zhang, R.

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Structure summary