6T9F | pdb_00006t9f

CRYSTAL STRUCTURE OF EN ENDOGLUCANASE S308P FROM PENICILLIUM VERRUCULOSUM

• PDB DOI: https://doi.org/10.2210/pdb6T9F/pdb

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


• Deposited: 2019-10-28 Released: 2020-11-18 
• Deposition Author(s): Nemashkalov, V., Kravchenko, O., Gabdulkhakov, A., Tischenko, S., Rozhkova, A., Sinitsyn, A.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF EN ENDOGLUCANASE S308P 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: 139.91 kDa 
• Atom Count: 9,631 
• Modeled Residue Count: 1,217 
• 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): 1  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	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	G [auth B], H [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.358	α = 81.807
b = 77.391	β = 76.69
c = 90.923	γ = 75.864

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Nemashkalov, V., Kravchenko, O., Gabdulkhakov, A., Tischenko, S., Rozhkova, A., Sinitsyn, A.

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

Revision History  

• Version 1.0: 2020-11-18
  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