3Q5V | pdb_00003q5v

The structure of inorganic pyrophosphatase from Thermococcus Thioreducens in complex with magnesium and sulfate

• PDB DOI: https://doi.org/10.2210/pdb3Q5V/pdb

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


• Deposited: 2010-12-29 Released: 2012-01-04 
• Deposition Author(s): Hughes, R.C., Coates, L., Meehan, E.J., Ng, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.155 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.122 (Depositor) 

Starting Model: experimental

Literature

The structure of inorganic pyrophosphatase from Thermococcus Thioreducens in complex with magnesium and sulfate

Hughes, R.C., Coates, L., Meehan, E.J., 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: 42.22 kDa 
• Atom Count: 4,091 
• Modeled Residue Count: 354 
• 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 H2L2L6 (Thermococcus thioreducens) Explore H2L2L6  Go to UniProtKB:  H2L2L6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A], G [auth A], H [auth B], J [auth B], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.155 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.122 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.49	α = 90
b = 114.49	β = 90
c = 148.6	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Hughes, R.C., Coates, L., Meehan, E.J., Ng, J.D.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description