5BWF | pdb_00005bwf

Crystal structure of the beta-glucosidase from Trichoderma harzianum

• PDB DOI: https://doi.org/10.2210/pdb5BWF/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma harzianum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-07 Released: 2016-07-06 
• Deposition Author(s): Santos, C.A., Zanphorlin, L.M., Crucello, A., Tonoli, C.C.C., Ruller, R., Souza, A.P., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the beta-glucosidase from Trichoderma harzianum

Santos, C.A., Zanphorlin, L.M., Crucello, A., Tonoli, C.C.C., Ruller, R., Souza, A.P., Murakami, M.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.05 kDa 
• Atom Count: 7,803 
• Modeled Residue Count: 942 
• Deposited Residue Count: 970 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,4-glucosidase	A, B	485	Trichoderma harzianum	Mutation(s): 0  Gene Names: bgl2 EC: 3.2.1.21
UniProt
Find proteins for A3FPG4 (Trichoderma harzianum) Explore A3FPG4  Go to UniProtKB:  A3FPG4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.241	α = 90
b = 218.241	β = 90
c = 84.675	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Santos, C.A., Zanphorlin, L.M., Crucello, A., Tonoli, C.C.C., Ruller, R., Souza, A.P., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/13309-0

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description