3R5V | pdb_00003r5v

The structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K

• PDB DOI: https://doi.org/10.2210/pdb3R5V/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., Meehan, E.J., Coates, L., Ng, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.163 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Starting Model: experimental

Literature

The structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K

Hughes, R.C., Meehan, E.J., Coates, L., 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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 125.88 kDa 
• Atom Count: 9,871 
• Modeled Residue Count: 1,047 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	J [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD	I [auth C], O [auth F]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
CA	G [auth A], H [auth B], K [auth C], L [auth D], M [auth E], N [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.163 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.092	α = 90
b = 95.564	β = 98.1
c = 113.769	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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