3PT1 | pdb_00003pt1

Structure of DUF89 from Saccharomyces cerevisiae co-crystallized with F6P.

• PDB DOI: https://doi.org/10.2210/pdb3PT1/pdb

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


• Deposited: 2010-12-02 Released: 2010-12-15 
• Deposition Author(s): Petit, P., Xu, X., Cui, H., Savchenko, A., Yakunin, A.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.192 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Structure and activity of a DUF89 protein from Saccharomyces cerevisiae revealed a novel family of carbohydrate phosphatases

Brown, G., Xu, X., Petit, P., Cui, H., Flick, R., Cuff, M., Savchenko, A., Yakunin, A.F.

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: 55.04 kDa 
• Atom Count: 4,098 
• Modeled Residue Count: 464 
• Deposited Residue Count: 471 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0364 protein YMR027W	A	471	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YM9711.17, YMR027W EC: 3.1.3
UniProt
Find proteins for Q04371 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04371  Go to UniProtKB:  Q04371

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F6P	C [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.192 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.32	α = 90
b = 108.65	β = 96.84
c = 88.08	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Petit, P., Xu, X., Cui, H., Savchenko, A., Yakunin, A.F.

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary