5AE6

The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1) in complex with 4-thioxylobiose

• PDB DOI: https://doi.org/10.2210/pdb5AE6/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Mutation(s): No 


• Deposited: 2015-08-26 Released: 2016-09-21 
• Deposition Author(s): Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Hansson, H., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.214 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Th Crystal Structure of a Fungal Glycoside Hydrolase Family 3 Beta-Xylosidase, Xyl3A from Hypocrea Jecorina

Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T., Hansson, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 176.48 kDa 
• Atom Count: 13,404 
• Modelled Residue Count: 1,529 
• Deposited Residue Count: 1,534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-XYLOSIDASE	A, B	767	Trichoderma reesei	Mutation(s): 0  EC: 3.2.1.37
UniProt
Find proteins for Q92458 (Hypocrea jecorina) Explore Q92458  Go to UniProtKB:  Q92458

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, H, I, K	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-4-deoxy-4-thio-alpha-D-xylopyranose	G, L	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G58687LH GlyCosmos:  G58687LH

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42227JK GlyCosmos:  G42227JK GlyGen:  G42227JK

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.214 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.244	α = 90
b = 202.443	β = 90
c = 82.441	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Hansson, H., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-03-11
  Changes: Data collection, Derived calculations, Other, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary