6TZY | pdb_00006tzy

Crystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase

• PDB DOI: https://doi.org/10.2210/pdb6TZY/pdb

• Classification: HYDROLASE
• Organism(s): Tetrahymena thermophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-13 Released: 2020-03-18 
• Deposition Author(s): Khayyo, V.I., Airola, M.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase

Khayyo, V.I., Hoffmann, R.M., Wang, H., Bell, J.A., Burke, J.E., Reue, K., Airola, M.V.

(2020) Nat Commun 11: 1309

• DOI: https://doi.org/10.1038/s41467-020-15124-z

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 147.14 kDa 
• Atom Count: 8,653 
• Modeled Residue Count: 1,063 
• Deposited Residue Count: 1,284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear elongation and deformation protein	A, B, C, D	321	Tetrahymena thermophila	Mutation(s): 0  Gene Names: TTHERM_00215970
UniProt
Find proteins for I7MFJ3 (Tetrahymena thermophila (strain SB210)) Explore I7MFJ3  Go to UniProtKB:  I7MFJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B], G [auth B], H [auth C], I [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.268 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.017	α = 90
b = 135.126	β = 116.19
c = 90.974	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Khayyo, V.I., Airola, M.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM128666
American Heart Association	United States	17SDG33410860
American Heart Association	United States	19PRE34450192

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description