7AKQ | pdb_00007akq

Structure of D169A/E171A double mutant of chitinase Chit42 from Trichoderma harzianum complexed with chitintetraose obtained by soaking.

• PDB DOI: https://doi.org/10.2210/pdb7AKQ/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma harzianum
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2020-10-01 Released: 2021-10-20 
• Deposition Author(s): Jimenez-Ortega, E., Sanz-Aparicio, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural inspection and protein motions modelling of a fungal glycoside hydrolase family 18 chitinase by crystallography depicts a dynamic enzymatic mechanism

Jimenez-Ortega, E., Kidibule, P.E., Fernandez-Lobato, M., Sanz-Aparicio, J.

(2021) Comput Struct Biotechnol J 19: 5466-5478

• DOI: https://doi.org/10.1016/j.csbj.2021.09.027

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 47.61 kDa 
• Atom Count: 3,299 
• Modeled Residue Count: 389 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endochitinase 42	A	423	Trichoderma harzianum	Mutation(s): 4  Gene Names: chit42 EC: 3.2.1.14
UniProt
Find proteins for P48827 (Trichoderma harzianum) Explore P48827  Go to UniProtKB:  P48827

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.111	α = 90
b = 68.111	β = 90
c = 176.639	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-20 
Deposition Author(s): Jimenez-Ortega, E., Sanz-Aparicio, J.

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description