4ECP | pdb_00004ecp

X-ray crystal structure of Inorganic Pyrophosphate PPA from Mycobacterium leprae

• PDB DOI: https://doi.org/10.2210/pdb4ECP/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium leprae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-26 Released: 2012-04-18 
• Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of Inorganic Pyrophosphate PPA from Mycobacterium leprae

Fairman, J.W., Abendroth, J., Staker, B.L., Stewart, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.1 kDa 
• Atom Count: 2,782 
• Modeled Residue Count: 322 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B	167	Mycobacterium leprae	Mutation(s): 0  Gene Names: ppa, ML0210, MLCB2548.21 EC: 3.6.1.1
UniProt
Find proteins for O69540 (Mycobacterium leprae (strain TN)) Explore O69540  Go to UniProtKB:  O69540

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34ECP

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.18	α = 90
b = 121.18	β = 90
c = 66.34	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description