4LUG | pdb_00004lug

Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb4LUG/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-25 Released: 2014-07-30 
• Deposition Author(s): Grzechowiak, M., Ruszkowski, M., Sikorski, M., Jaskolski, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Inorganic pyrophosphatase PPA1 from Arabidopsis thaliana

Grzechowiak, M., Ruszkowski, M., Sikorski, M., Jaskolski, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.63 kDa 
• Atom Count: 3,015 
• Modeled Residue Count: 351 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B	180	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PPa1 EC: 3.6.1.1
UniProt
Find proteins for Q93V56 (Arabidopsis thaliana) Explore Q93V56  Go to UniProtKB:  Q93V56

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.02	α = 90
b = 82.02	β = 90
c = 175.08	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Grzechowiak, M., Ruszkowski, M., Sikorski, M., Jaskolski, M.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description