1SXV | pdb_00001sxv

1.3A Crystal structure of rv3628, Mycobacterium tuberculosis inorganic pyrophosphatase (PPase) at pH5.0

• PDB DOI: https://doi.org/10.2210/pdb1SXV/pdb

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


• Deposited: 2004-03-31 Released: 2005-04-12 
• Deposition Author(s): Benini, S., Wilson, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Mycobacterium tuberculosis Rv3628, yet another inorganic pyrophosphatase or a possible drug target?

Benini, S., Wilson, K.S.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 19.92 kDa 
• Atom Count: 1,619 
• Modeled Residue Count: 160 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A	172	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: PPA, RV3628, MT3730, MTCY15C10.24, MB3652 EC: 3.6.1.1
UniProt
Find proteins for P9WI55 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI55  Go to UniProtKB:  P9WI55

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.46	α = 90
b = 98.46	β = 90
c = 97.353	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Benini, S., Wilson, K.S.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description