6JDY

Ligand complex structure of GH10 family xylanase XynAF1, soaking for 120 minutes

• PDB DOI: https://doi.org/10.2210/pdb6JDY/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: 1.50 Å
• R-Value Free: 0.151 
• R-Value Work: 0.121 
• R-Value Observed: 0.123 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.57 kDa 
• Atom Count: 5,708 
• Modelled 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, D, E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	J [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	C, D, E, F	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.151 
• R-Value Work: 0.121 
• R-Value Observed: 0.123 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.33	α = 74.19
b = 57.106	β = 80.96
c = 64.734	γ = 68.87

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary