8W4X | pdb_00008w4x

Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, Enzyme-Product complex

• PDB DOI: https://doi.org/10.2210/pdb8W4X/pdb

• Classification: HYDROLASE
• Organism(s): Phanerodontia chrysosporium
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2023-08-25 Released: 2025-03-12 
• Deposition Author(s): Tachioka, M., Yamaguchi, S., Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Yano, N., Chatake, T., Tamada, T., Takeda, K., Niwa, S., Tanaka, H., Takahashi, S., Inaka, K., Furubayashi, N., Deguchi, S., Samejima, M., Igarashi, K.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.139 (Depositor), 0.139 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.166 (Depositor) 
• R-Value Work: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase

Tachioka, M., Yamaguchi, S., Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Yano, N., Chatake, T., Tamada, T., Takeda, K., Niwa, S., Tanaka, H., Takahashi, S., Inaka, K., Furubayashi, N., Deguchi, S., Samejima, M., Igarashi, K.

To be published.

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: 38.93 kDa 
• Atom Count: 3,143 
• Modelled 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): 0  Gene Names: cel6A EC: 3.2.1
UniProt
Find proteins for H3K419 (Phanerodontia chrysosporium) Explore H3K419  Go to UniProtKB:  H3K419

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B [auth C]	2	N/A	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC (Subject of Investigation/LOI)	C [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900023	B [auth C]	alpha-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.139 (Depositor), 0.139 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.166 (Depositor) 
• R-Value Work:  0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.73	α = 90
b = 68.26	β = 90
c = 89.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
STARGazer	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Tachioka, M., Yamaguchi, S., Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Yano, N., Chatake, T., Tamada, T., Takeda, K., Niwa, S., Tanaka, H., Takahashi, S., Inaka, K., Furubayashi, N., Deguchi, S., Samejima, M., Igarashi, K.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18H05494
Japan Society for the Promotion of Science (JSPS)	Japan	23H00341, 19H03013, 18J01906, 15J10657

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release