1M38

Structure of Inorganic Pyrophosphatase

• PDB DOI: https://doi.org/10.2210/pdb1M38/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2002-06-27 Released: 2003-01-28 
• Deposition Author(s): Kuranova, I.P., Polyakov, K.M., Levdikov, V.M., Smirnova, E.A., Hohne, W.E., Lamzin, V.S., Meijers, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions

Kuranova, I.P., Polyakov, K.M., Smirnova, E.A., Hohne, W.E., Lamzin, V.S., Meijers, R.

(2003) Crystallogr Rep 48: 953-958

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 65.22 kDa 
• Atom Count: 5,234 
• Modelled Residue Count: 564 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INORGANIC PYROPHOSPHATASE	A, B	287	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.6.1.1
UniProt
Find proteins for P00817 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00817  Go to UniProtKB:  P00817

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CO	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.69	α = 90
b = 93.23	β = 99.74
c = 69.84	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
BLANC	model building
REFMAC	refinement
CCP4	data scaling
BLANC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-28 
Deposition Author(s): Kuranova, I.P., Polyakov, K.M., Levdikov, V.M., Smirnova, E.A., Hohne, W.E., Lamzin, V.S., Meijers, R.

Revision History  

• Version 1.0: 2003-01-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations