3R6E | pdb_00003r6e

The structure of Thermococcus thioreducens' inorganic pyrophosphatase bound to sulfate

• PDB DOI: https://doi.org/10.2210/pdb3R6E/pdb

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


• Deposited: 2011-03-21 Released: 2012-03-28 
• Deposition Author(s): Hughes, R.C., Meehan, E.J., Ng, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.148 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

Literature

The structure of Thermococcus thioreducens' inorganic pyrophosphatase bound to sulfate

Hughes, R.C., 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: 127.95 kDa 
• Atom Count: 11,573 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tt-IPPase	A, B, C, D, E, F	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth D], M [auth D], O [auth E], P [auth E], Q [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NH4	N [auth D]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.148 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.776	α = 105.92
b = 67.283	β = 106.58
c = 74.139	γ = 101.92

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.2: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary