2UXS | pdb_00002uxs

2.7A crystal structure of inorganic pyrophosphatase (Rv3628) from Mycobacterium tuberculosis at pH 7.5

• PDB DOI: https://doi.org/10.2210/pdb2UXS/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-29 Released: 2008-05-27 
• Deposition Author(s): Cole, R.E., Cianci, M., Hall, J.F., Matsuda, T., Kigawa, T., Yokoyama, S., Hasnain, S.S., Tabernero, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.274 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Rv3628: An Inorganic Pyrophosphatase from Mycobacterium Tuberculosis

Cole, R.E., Cianci, M., Hall, J.F., Matsuda, T., Kigawa, T., Yokoyama, S., Hasnain, S.S., Tabernero, 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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 56.81 kDa 
• Atom Count: 3,879 
• Modeled Residue Count: 480 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INORGANIC PYROPHOSPHATASE	A, B, C	169	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.274 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.022	α = 90
b = 102.022	β = 90
c = 80.812	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Cole, R.E., Cianci, M., Hall, J.F., Matsuda, T., Kigawa, T., Yokoyama, S., Hasnain, S.S., Tabernero, L.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description