6YON | pdb_00006yon

Crystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum

• PDB DOI: https://doi.org/10.2210/pdb6YON/pdb

• Classification: HYDROLASE
• Organism(s): Talaromyces verruculosus
• Expression System: Penicillium canescens
• Mutation(s): Yes 


• Deposited: 2020-04-14 Released: 2021-04-28 
• Deposition Author(s): Nemashkalov, V., Kravchenko, O., Gabdulkhakov, A., Tischenko, S., Rozhkova, A., Sinitsyn, A.
• Funding Organization(s): Russian Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.292 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum

Nemashkalov, V., Kravchenko, O., Gabdulkhakov, A., Tischenko, S., Rozhkova, A., Sinitsyn, A.

To be published.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.86 kDa 
• Atom Count: 9,645 
• Modeled Residue Count: 1,220 
• Deposited Residue Count: 1,256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A, B, C, D	314	Talaromyces verruculosus	Mutation(s): 4  EC: 3.2.1.4
UniProt
Find proteins for A0A1U7Q1U3 (Talaromyces verruculosus) Explore A0A1U7Q1U3  Go to UniProtKB:  A0A1U7Q1U3
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.292 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.5	α = 90
b = 85.69	β = 89.99
c = 91.15	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Nemashkalov, V., Kravchenko, O., Gabdulkhakov, A., Tischenko, S., Rozhkova, A., Sinitsyn, A.

---

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	--

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary