5M4A

Neutral trehalase Nth1 from Saccharomyces cerevisiae in complex with trehalose

• PDB DOI: https://doi.org/10.2210/pdb5M4A/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-18 Released: 2017-11-01 
• Deposition Author(s): Smidova, A., Alblova, M., Obsilova, V., Obsil, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

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: 69.46 kDa 
• Atom Count: 4,360 
• Modelled Residue Count: 548 
• Deposited Residue Count: 603 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutral trehalase	A	603	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: NTH1, NTH, YDR001C, YD8119.07C EC: 3.2.1.28
UniProt
Find proteins for P32356 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32356  Go to UniProtKB:  P32356

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	B	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.769	α = 90
b = 185.769	β = 90
c = 118.799	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Smidova, A., Alblova, M., Obsilova, V., Obsil, T.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary