1RII

Crystal structure of phosphoglycerate mutase from M. Tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb1RII/pdb

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


• Deposited: 2003-11-17 Released: 2004-10-05 
• Deposition Author(s): Mueller, P., Sawaya, M.R., Chan, S., Wu, Y., Pashkova, I., Perry, J., Eisenberg, D., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.270 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.

Muller, P., Sawaya, M.R., Pashkov, I., Chan, S., Nguyen, C., Wu, Y., Perry, L.J., Eisenberg, D.

(2005) Acta Crystallogr D Biol Crystallogr 61: 309-315

• PubMed: 15735341 
• DOI: https://doi.org/10.1107/S0907444904033190
• Primary Citation of Related Structures:  
  1RII


• PubMed Abstract: 
  

  The single-crystal X-ray structure of phosphoglycerate mutase from Mycobacterium tuberculosis has been determined at a resolution of 1.70 angstroms. The C-terminal tail of each of the subunits is flexible and disordered; however, for one of the four chains (chain A) all but five residues of the chain could be modeled. Noteworthy features of the structure include the active site and a proline-rich segment in each monomer forming a short left-handed polyprolyl helix. These segments lie on the enzyme surface and could conceivably participate in protein-protein interactions.

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Organizational Affiliation: 

UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, Box 951570, Los Angeles, CA 90095-1570, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 116.46 kDa 
• Atom Count: 7,910 
• Modelled Residue Count: 948 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase	A, B, C, D	265	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: GPMA, GPM, PGM, GPM1, RV0489, MT0508, MTCY20G9.15, MB0499 EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
UniProt
Find proteins for P9WIC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIC9  Go to UniProtKB:  P9WIC9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth D], H [auth D], I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.270 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.914	α = 90
b = 136.79	β = 97.78
c = 65.929	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SADABS	data reduction
GLRF	phasing
SHELXL-97	refinement
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-05 
Deposition Author(s): Mueller, P., Sawaya, M.R., Chan, S., Wu, Y., Pashkova, I., Perry, J., Eisenberg, D., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description