7ZON

Carbohydrate binding domain CBMXX from a multi-catalytic glucanase-chitinase from Chitinophaga pinensis DSM 2588 in complex with glucose

• PDB DOI: https://doi.org/10.2210/pdb7ZON/pdb

• Classification: CARBOHYDRATE
• Organism(s): Chitinophaga pinensis DSM 2588
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-04-26 Released: 2023-05-10 
• Deposition Author(s): Mazurkewich, S., McKee, L.S., Lu, Z., Branden, G., Larsbrink, J.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.235 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

CBMXX: A new family of Carbohydrate Binding Modules displaying three distinct ligand binding sites with affinity for beta-glucans.

Mazurkewich, S., McKee, L.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.31 kDa 
• Atom Count: 2,144 
• Modelled Residue Count: 253 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbohydrate binding domain XX	A, B	147	Chitinophaga pinensis DSM 2588	Mutation(s): 1
UniProt
Find proteins for A0A979GQH9 (Chitinophaga pinensis (strain ATCC 43595 / DSM 2588 / LMG 13176 / NBRC 15968 / NCIMB 11800 / UQM 2034)) Explore A0A979GQH9  Go to UniProtKB:  A0A979GQH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
BGC (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A, B	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.235 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.082	α = 90
b = 111.97	β = 100.322
c = 71.306	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Mazurkewich, S., McKee, L.S., Lu, Z., Branden, G., Larsbrink, J.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2017-04906
Knut and Alice Wallenberg Foundation	Sweden	WWSC

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-02-07
  Changes: Refinement description