8A8F

Crystal structure of Glc7 phosphatase in complex with the regulatory region of Ref2

• PDB DOI: https://doi.org/10.2210/pdb8A8F/pdb

• Classification: GENE REGULATION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-06-22 Released: 2023-11-29 
• Deposition Author(s): Carminati, M., Manav, C.M., Bellini, D., Passmore, L.A.
• Funding Organization(s): European Union (EU), European Molecular Biology Organization (EMBO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Crystal structure of Glc7 phosphatase in complex with the regulatory region of Ref2

Carminati, M., Manav, C.M., Bellini, D., Passmore, L.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.74 kDa 
• Atom Count: 2,986 
• Modelled Residue Count: 354 
• Deposited Residue Count: 393 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase PP1-2	A	313	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: GLC7, CID1, DIS2, YER133W EC: 3.1.3.16
UniProt
Find proteins for P32598 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32598  Go to UniProtKB:  P32598

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA end formation protein 2	B	80	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: REF2, YDR195W, YD9346.06
UniProt
Find proteins for P42073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42073  Go to UniProtKB:  P42073

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.23	α = 90
b = 90.23	β = 90
c = 101.14	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Carminati, M., Manav, C.M., Bellini, D., Passmore, L.A.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	725685
European Molecular Biology Organization (EMBO)	European Union	556-2018

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release