9K7M

Coprinopsis cinerea GH131 protein CcGH131B E161A in complex with cellobiose

• PDB DOI: https://doi.org/10.2210/pdb9K7M/pdb

• Classification: HYDROLASE
• Organism(s): Coprinopsis cinerea okayama7#130
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-24 Released: 2024-11-06 
• Deposition Author(s): Shiojima, Y., Tonozuka, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.182 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Crystal structure of CcGH131B, a protein belonging to glycoside hydrolase family 131 from the basidiomycete Coprinopsis cinerea

Shiojima, Y., Tonozuka, T.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.65 kDa 
• Atom Count: 5,788 
• Modelled Residue Count: 604 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase 131 catalytic N-terminal domain-containing protein	A, B	313	Coprinopsis cinerea okayama7#130	Mutation(s): 3  Gene Names: CC1G_15039
UniProt
Find proteins for D6RP27 (Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003)) Explore D6RP27  Go to UniProtKB:  D6RP27

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G86802XL GlyCosmos:  G86802XL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth A], G [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE	H [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.182 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.66	α = 90
b = 71.66	β = 90
c = 226.521	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Shiojima, Y., Tonozuka, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24K08698
Japan Science and Technology	Japan	JPMJSP2116

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Database references, Structure summary