9GSR | pdb_00009gsr

Crystal Structure of M. hassiacum GPGS co-crystallized with UDP-Glucose (pH 7.2)

• PDB DOI: https://doi.org/10.2210/pdb9GSR/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium hassiacum DSM 44199
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-16 Released: 2025-09-24 
• Deposition Author(s): Macedo-Ribeiro, S., Nunes-Costa, D., Silva, A., Pereira, P.J.B.
• Funding Organization(s): Foundation for Science and Technology (FCT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of M. Hassiacum GPGS

Macedo-Ribeiro, S., Nunes-Costa, D.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.41 kDa 
• Atom Count: 5,097 
• Modeled Residue Count: 577 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyl-3-phosphoglycerate synthase	A, B	327	Mycolicibacterium hassiacum DSM 44199	Mutation(s): 0  Gene Names: gpgS, C731_3243, MHAS_02845 EC: 2.4.1.266
UniProt
Find proteins for K5B7Z4 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)) Explore K5B7Z4  Go to UniProtKB:  K5B7Z4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	D [auth A], E [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
TLA (Subject of Investigation/LOI)	C [auth A], F [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.371	α = 90
b = 90.548	β = 90
c = 95.307	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Macedo-Ribeiro, S., Nunes-Costa, D., Silva, A., Pereira, P.J.B.

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Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	Portugal	--

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release