3EIY

Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei with bound pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb3EIY/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-17 Released: 2008-09-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

The role of medical structural genomics in discovering new drugs for infectious diseases.

Van Voorhis, W.C., Hol, W.G., Myler, P.J., Stewart, L.J.

(2009) PLoS Comput Biol 5: e1000530-e1000530

• PubMed: 19855826 
• DOI: https://doi.org/10.1371/journal.pcbi.1000530
• Primary Citation of Related Structures:  
  3EIY, 3EJ0

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Organizational Affiliation: 

Department of Medicine, University of Washington, Seattle, Washington, United States of America.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.14 kDa 
• Atom Count: 1,481 
• Modelled Residue Count: 174 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A	196	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: ppa, BURPS1710b_1237 EC: 3.6.1.1
UniProt
Find proteins for Q3JUV5 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JUV5  Go to UniProtKB:  Q3JUV5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
POP	E [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
PEG	G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.952	α = 90
b = 100.952	β = 90
c = 111.233	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-05
  Changes: Database references
• Version 1.3: 2013-10-23
  Changes: Database references
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations