4W87

Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library, in complex with a xyloglucan oligosaccharide

• PDB DOI: https://doi.org/10.2210/pdb4W87/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-08-22 Released: 2015-03-11 
• Deposition Author(s): Santos, C.R., Cordeiro, R.L., Wong, D.W.S., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Biological Assembly 1  

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

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

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: 77.56 kDa 
• Atom Count: 5,747 
• Modelled Residue Count: 678 
• Deposited Residue Count: 678 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xyloglucan-specific endo-beta-1,4-glucanase	A, B	339	uncultured bacterium	Mutation(s): 1  EC: 3.2.1.151
UniProt
Find proteins for D2K7Z0 (uncultured bacterium) Explore D2K7Z0  Go to UniProtKB:  D2K7Z0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	4		N/A
Glycosylation Resources
GlyTouCan:  G55895NR GlyCosmos:  G55895NR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.504	α = 90
b = 96.504	β = 90
c = 95.857	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Santos, C.R., Cordeiro, R.L., Wong, D.W.S., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/13309-0, 2014/07135-1

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-03-25
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.3: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Structure summary