3I98 | pdb_00003i98

X-ray crystallographic structure of Inorganic Pyrophosphatase at 298K from archaeon Thermococcus thioreducens

• PDB DOI: https://doi.org/10.2210/pdb3I98/pdb

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


• Deposited: 2009-07-10 Released: 2009-08-18 
• 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: 1.85 Å
• R-Value Free: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallographic structure of Inorganic Pyrophosphatase at 298K from archaeon Thermococcus thioreducens

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)

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: 125.92 kDa 
• Atom Count: 10,184 
• Modeled Residue Count: 1,049 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 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	G [auth A], P [auth F]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
ACE	M [auth E]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N
CA	H [auth A], I [auth B], K [auth C], L [auth D], N [auth E], O [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.112	α = 90
b = 95.464	β = 98.12
c = 113.677	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Hughes, R.C., Coates, L., Meehan, E.J., Ng, J.D.

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model, Non-polymer description
• Version 1.3: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.4: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Experimental preparation, Refinement description