5TY5

Neutron structure from microgravity-grown crystals of Inorganic Pyrophosphatase from Thermococcus theoreducens

• PDB DOI: https://doi.org/10.2210/pdb5TY5/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus thioreducens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-18 Released: 2017-11-22 
• Deposition Author(s): Inoguchi, N., Coates, L., Morris, M.L., Singhal, A., Monaco, D.A., Garcia-Ruiz, J.M., Pusey, M.L., Ng, J.D.
• Funding Organization(s): Center for the Advancement of Science in Space (CASIS)

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Literature

Structure-function analysis of the neutron crystallographic structure of inorganic pyrophosphatase determined from microgravity-grown crystals

Inoguchi, N., Coates, L., Meilleur, F., Morris, M.L., Singhal, A., Barcena, J., Garcia-Ruiz, J.M., Pusey, M.L., Ng, J.D.

(2017) Acta Crystallogr A 73: 132-132

• DOI: https://doi.org/10.1107/S0108767317098695

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: 125.29 kDa 
• Atom Count: 9,025 
• Modelled Residue Count: 1,044 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B, C, D, E, F	178	Thermococcus thioreducens	Mutation(s): 0  Gene Names: ppa EC: 3.6.1.1
UniProt
Find proteins for H0USY5 (Thermococcus thioreducens) Explore H0USY5  Go to UniProtKB:  H0USY5

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.93	α = 90
b = 95.03	β = 98.13
c = 113.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
LAUENORM	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Inoguchi, N., Coates, L., Morris, M.L., Singhal, A., Monaco, D.A., Garcia-Ruiz, J.M., Pusey, M.L., Ng, J.D.

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Funding Organization	Location	Grant Number
Center for the Advancement of Science in Space (CASIS)	United States	GA-2013-100

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2019-01-09
  Changes: Data collection, Database references, Experimental preparation
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description