7PDO | pdb_00007pdo

Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with UDP

• PDB DOI: https://doi.org/10.2210/pdb7PDO/pdb

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


• Deposited: 2021-08-05 Released: 2023-02-15 
• Deposition Author(s): Silva, A., Nunes-Costa, D., Barbosa Pereira, P.J., Macedo-Ribeiro, S.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with UDP

Silva, A., Nunes-Costa, D., Empadinhas, N., Barbosa Pereira, P.J., Macedo-Ribeiro, S.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.56 kDa 
• Atom Count: 2,498 
• Modeled Residue Count: 301 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyl-3-phosphoglycerate synthase	A	326	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]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
CL	B [auth A], C [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/992

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.338	α = 90
b = 101.338	β = 90
c = 122.532	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: 2023-02-15 
Deposition Author(s): Silva, A., Nunes-Costa, D., Barbosa Pereira, P.J., Macedo-Ribeiro, S.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BTM-TEC/29221/2017 (POCI-01-0145-FEDER-029221).

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references, Structure summary
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description