8X09 | pdb_00008x09

X-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/C393S soaked in methyl-cellobiosyl-4-deoxy-4-thio-beta-D-cellobioside

• PDB DOI: https://doi.org/10.2210/pdb8X09/pdb

• Classification: HYDROLASE
• Organism(s): Phanerodontia chrysosporium
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2023-11-04 Released: 2024-11-20 
• Deposition Author(s): Yamaguchi, S., Sunagawa, N., Tachioka, M., Igarashi, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Activity and X-ray crystal structure of candidate base catalyst mutants of glycoside hydrolase family 6 cellobiohydrolase

Yamaguchi, S., Sunagawa, N., Tachioka, M., Igarashi, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.73 kDa 
• Atom Count: 3,378 
• Modeled Residue Count: 358 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A	358	Phanerodontia chrysosporium	Mutation(s): 2  Gene Names: cel6A EC: 3.2.1
UniProt
Find proteins for Q02321 (Phanerodontia chrysosporium) Explore Q02321  Go to UniProtKB:  Q02321

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside	B	4	N/A	N/A
Glycosylation Resources
GlyTouCan:  G15263TL GlyCosmos:  G15263TL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A], D [auth A], F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.53	α = 90
b = 67.258	β = 90
c = 88.247	γ = 90

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: 2024-11-20 
Deposition Author(s): Yamaguchi, S., Sunagawa, N., Tachioka, M., Igarashi, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J12651

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release