6UB4

Crystal structure (C2 form) of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose

• PDB DOI: https://doi.org/10.2210/pdb6UB4/pdb

• Classification: HYDROLASE
• Organism(s): Lentinula edodes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-11 Released: 2020-05-20 
• Deposition Author(s): Santos, C.R., Lima, E.A., Mandelli, F., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

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: light scattering

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: 59.02 kDa 
• Atom Count: 4,541 
• Modelled Residue Count: 494 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSIDE HYDROLASE	A, B	270	Lentinula edodes	Mutation(s): 0  Gene Names: glu1
UniProt
Find proteins for G9M5R4 (Lentinula edodes) Explore G9M5R4  Go to UniProtKB:  G9M5R4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G00024MO GlyCosmos:  G00024MO GlyGen:  G00024MO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	D, E	2		N/A
Glycosylation Resources
GlyTouCan:  G36535HU GlyCosmos:  G36535HU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL	F [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024	D, E	beta-laminaribiose	Oligosaccharide / Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.775	α = 90
b = 46.52	β = 119.5
c = 114.786	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Santos, C.R., Lima, E.A., Mandelli, F., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	15/26982-0

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: 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: 2020-08-05
  Changes: Database references
• Version 2.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary