3R5U | pdb_00003r5u

The structure of manganese bound Thermococcus thioreducens Inorganic pyrophosphatase

• PDB DOI: https://doi.org/10.2210/pdb3R5U/pdb

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


• Deposited: 2011-03-19 Released: 2012-03-28 
• Deposition Author(s): Hughes, R.C., Coates, L., Meehan, E.J., Garcia-Ruiz, J.M., Ng, J.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

The structure of manganese bound Thermococcus thioreducens Inorganic pyrophosphatase

Hughes, R.C., Coates, L., Meehan, E.J., Garcia-Ruiz, J.M., Ng, J.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 41.87 kDa 
• Atom Count: 3,447 
• Modeled Residue Count: 350 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tt-IPPase	A, B	178	Thermococcus thioreducens	Mutation(s): 0  Gene Names: Tt-IPPase EC: 3.6.1.1
UniProt
Find proteins for H0USY5 (Thermococcus thioreducens) Explore H0USY5  Go to UniProtKB:  H0USY5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.514	α = 90
b = 114.514	β = 90
c = 148.438	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Hughes, R.C., Coates, L., Meehan, E.J., Garcia-Ruiz, J.M., Ng, J.D.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description