7EO3 | pdb_00007eo3

X-ray structure analysis of beita-1,3-glucanase

• PDB DOI: https://doi.org/10.2210/pdb7EO3/pdb

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


• Deposited: 2021-04-21 Released: 2022-03-02 
• Deposition Author(s): Wan, Q., Feng, J., Xu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Identification and structural analysis of a thermophilic beta-1,3-glucanase from compost

Feng, J., Xu, S., Feng, R., Kovalevsky, A., Zhang, X., Liu, D., Wan, Q.

(2021) Bioresour Bioprocess 8: 102-102

• DOI: https://doi.org/10.1186/s40643-021-00449-4

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: 31.01 kDa 
• Atom Count: 2,527 
• Modeled Residue Count: 282 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,3-beta-glucanase	A	283	Actinomycetes bacterium	Mutation(s): 0  Gene Names: DIU60_04100

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.397	α = 90
b = 61.01	β = 90
c = 70.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Wan, Q., Feng, J., Xu, S.

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary