6XQH

Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with cellotriose, presenting a 1,3-beta-D-cellobiosyl-glucose and a cellobiose at active site

• PDB DOI: https://doi.org/10.2210/pdb6XQH/pdb

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


• Deposited: 2020-07-09 Released: 2021-02-10 
• Deposition Author(s): Liberato, M.V., Squina, F.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.192 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 

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

Macromolecule Content

• Total Structure Weight: 31.18 kDa 
• Atom Count: 2,612 
• Modelled Residue Count: 260 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH16 family protein	A	269	uncultured bacterium	Mutation(s): 1  Gene Names: sclam EC: 3.2.1.39
UniProt
Find proteins for A0A0B5H9B3 (uncultured bacterium) Explore A0A0B5H9B3  Go to UniProtKB:  A0A0B5H9B3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G89925KE GlyCosmos:  G89925KE GlyGen:  G89925KE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	C	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.192 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.729	α = 90
b = 49.745	β = 90
c = 115.261	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Liberato, M.V., Squina, F.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/04105-4
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/50590-4
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	310177/2011-1

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2021-08-25
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description