5JQQ | pdb_00005jqq

Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis - apo form

• PDB DOI: https://doi.org/10.2210/pdb5JQQ/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-05 Released: 2016-12-21 
• Deposition Author(s): Albesa-Jove, D., Urresti, S., Gest, P.M., van der Woerd, M., Jackson, M., Guerin, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4DDZ

Literature

Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis - apo form

Albesa-Jove, D., Romero-Garcia, J., Sancho-Vaello, E., Contreras, F.-X., Rodrigo-Unzueta, A., Comino, N., Carreras-Gonzalez, A., Arrasate, P., Urresti, S., Biarnes, X., Planas, A., Guerin, M.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.77 kDa 
• Atom Count: 2,237 
• Modeled Residue Count: 276 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyl-3-phosphoglycerate synthase	A	344	Mycobacterium tuberculosis H37Ra	Mutation(s): 0  Gene Names: gpgS, Rv1208 EC: 2.4.1.266
UniProt
Find proteins for P9WMW9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMW9  Go to UniProtKB:  P9WMW9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.209 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.85	α = 90
b = 98.85	β = 90
c = 127.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Albesa-Jove, D., Urresti, S., Gest, P.M., van der Woerd, M., Jackson, M., Guerin, M.E.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-12-10
  Changes: Structure summary