7QWJ | pdb_00007qwj

Crystal structure of Glc7 phosphatase

• PDB DOI: https://doi.org/10.2210/pdb7QWJ/pdb

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-25 Released: 2023-02-01 
• Deposition Author(s): Malhotra, K., Carminati, M., Bertolotti, A., Bellini, D.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Glc7 phosphatase

Bellini, D., Malhotra, K., Carminati, M., Bertolotti, A.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.18 kDa 
• Atom Count: 2,503 
• Modeled Residue Count: 298 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase PP1-2	A	313	Saccharomyces cerevisiae S288C	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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.284	α = 90
b = 83.294	β = 90
c = 96.532	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Malhotra, K., Carminati, M., Bertolotti, A., Bellini, D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	206367/Z/17/Z

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description