5H9Y | pdb_00005h9y

Crystal structure of GH family 64 laminaripentaose-producing beta-1,3-glucanase from Paenibacillus barengoltzii complexed with laminarihexaose.

• PDB DOI: https://doi.org/10.2210/pdb5H9Y/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus barengoltzii
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-12-29 Released: 2017-02-15 
• Deposition Author(s): Zhen, Q., Yan, Q., Yang, S., Jiang, Z., You, X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

The recognition mechanism of triple-helical beta-1,3-glucan by a beta-1,3-glucanase

Qin, Z., Yang, D., You, X., Liu, Y., Hu, S., Yan, Q., Yang, S., Jiang, Z.

(2017) Chem Commun (Camb) 53: 9368-9371

• PubMed: 28787048 
• DOI: https://doi.org/10.1039/c7cc03330c
• Primary Citation Related Structures: 
  5H9X, 5H9Y


• PubMed Abstract: 
  

  β-1,3-Glucan is one of the most abundant polysaccharides in fungi. Recognition of β-1,3-glucan occurs in both hydrolysis by glycoside hydrolases and immunological recognition. Our study provides a novel structural account of how glycoside hydrolase recognizes and hydrolyzes substrates in a triple-helical form and presents a general structural basis of β-1,3-glucan recognition.

---

Organizational Affiliation: 
• Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.66 kDa 
• Atom Count: 3,876 
• Modeled Residue Count: 412 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-1,3-glucanase	A	444	Paenibacillus barengoltzii	Mutation(s): 0  EC: 3.2.1.39
UniProt
Find proteins for A0A1S4NYE2 (Paenibacillus barengoltzii) Explore A0A1S4NYE2  Go to UniProtKB:  A0A1S4NYE2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan: G03330ED GlyCosmos: G03330ED

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan: G87841AX GlyCosmos: G87841AX GlyGen: G87841AX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.561	α = 90
b = 65.191	β = 104.04
c = 61.426	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Zhen, Q., Yan, Q., Yang, S., Jiang, Z., You, X.

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary