7ZGG | pdb_00007zgg

Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, phosphate-bound

• PDB DOI: https://doi.org/10.2210/pdb7ZGG/pdb

• Classification: HYDROLASE
• Organism(s): Amycolatopsis jejuensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-03 Released: 2022-05-18 
• Deposition Author(s): Acquistapace, I.M., Brearley, C.A., Hemmings, A.M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, apo-protein

Acquistapace, I.M., Brearley, C.A., Hemmings, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.03 kDa 
• Atom Count: 7,421 
• Modeled Residue Count: 824 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multiple inositol-polyphosphate phosphatase	A, B	417	Amycolatopsis jejuensis	Mutation(s): 0  EC: 3.1.3.62 (PDB Primary Data), 3.1.3.80 (UniProt)
UniProt
Find proteins for A0A915Q9M0 (Amycolatopsis jejuensis) Explore A0A915Q9M0  Go to UniProtKB:  A0A915Q9M0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.887	α = 90
b = 86.91	β = 97.928
c = 70.54	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Acquistapace, I.M., Brearley, C.A., Hemmings, A.M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M022978/1

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary