3WFL | pdb_00003wfl

Crtstal structure of glycoside hydrolase family 5 beta-mannanase from Talaromyces trachyspermus

• PDB DOI: https://doi.org/10.2210/pdb3WFL/pdb

• Classification: HYDROLASE
• Organism(s): Talaromyces trachyspermus
• Mutation(s): No 


• Deposited: 2013-07-19 Released: 2014-07-23 
• Deposition Author(s): Suzuki, K., Ichinose, H., Kamino, K., Ogasawara, W., Kaneko, S., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.138 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.114 (Depositor) 
• R-Value Observed: 
  0.115 (Depositor) 

Starting Model: experimental

Literature

Purification, cloning, functional expression, structure, and characterization of a thermostable beta-mannanase from Talaromyces trachyspermus and its efficiency in production of mannooligosaccharides from coffee wastes

Ichinose, H., Suzuki, K., Yuki, M., Michikawa, M., Sato, H., Kamino, K., Ogasawara, W., Fushinobu, S., Kaneko, S.

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)

Macromolecule Content 

• Total Structure Weight: 38.27 kDa 
• Atom Count: 3,128 
• Modeled Residue Count: 341 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-mannanase	A	342	Talaromyces trachyspermus	Mutation(s): 0  EC: 3.2.1.78
UniProt
Find proteins for A0A087WNH1 (Talaromyces trachyspermus) Explore A0A087WNH1  Go to UniProtKB:  A0A087WNH1
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4	K [auth A], L [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.138 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.114 (Depositor) 
• R-Value Observed: 0.115 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.434	α = 90
b = 75.972	β = 90
c = 79.723	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Suzuki, K., Ichinose, H., Kamino, K., Ogasawara, W., Kaneko, S., Fushinobu, S.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-09
  Changes: Structure summary