5GLQ

Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose and xylotriose, calcium-free form

• PDB DOI: https://doi.org/10.2210/pdb5GLQ/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-12 Released: 2017-03-15 
• Deposition Author(s): Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K.
• Funding Organization(s): New Energy and Industrial Technology Development Organization (NEDO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.175 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78.15 kDa 
• Atom Count: 5,918 
• Modelled Residue Count: 655 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 43	A, B	344	uncultured bacterium	Mutation(s): 0  Gene Names: coxyl43
UniProt
Find proteins for A0A0H5BL38 (uncultured bacterium) Explore A0A0H5BL38  Go to UniProtKB:  A0A0H5BL38

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	D	3		N/A
Glycosylation Resources
GlyTouCan:  G87429QT GlyCosmos:  G87429QT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUB	G [auth A], J [auth B]	beta-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-KLVWXMOXSA-N
NA	E [auth A], F [auth A], H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

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

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117	D	4beta-beta-xylotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.175 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.801	α = 90
b = 61.489	β = 95.72
c = 79.047	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Matsuzawa, T., Kishine, N., Fujimoto, Z., Yaoi, K.

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Funding Organization	Location	Grant Number
New Energy and Industrial Technology Development Organization (NEDO)	Japan	--

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary