3SW5 | pdb_00003sw5

Crystal structure of inorganic pyrophosphatase from Bartonella henselae

• PDB DOI: https://doi.org/10.2210/pdb3SW5/pdb

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


• Deposited: 2011-07-13 Released: 2011-08-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of inorganic pyrophosphatase from Bartonella henselae

SSGCID, Gardberg, A., Clifton, M.C., Staker, B., Stewart, L.

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: 122.91 kDa 
• Atom Count: 8,335 
• Modeled Residue Count: 1,033 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B, C, D, E, F	180	Bartonella henselae	Mutation(s): 0  Gene Names: ppa, BH01690 EC: 3.6.1.1
UniProt
Find proteins for A0A0H3M4F9 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore A0A0H3M4F9  Go to UniProtKB:  A0A0H3M4F9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMR	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	(2S)-2-hydroxybutanedioic acid C4 H6 O5 BJEPYKJPYRNKOW-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33SW5

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.86	α = 90.37
b = 68.96	β = 113.38
c = 74.48	γ = 119.79

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-10-22
  Changes: Structure summary