4M2A | pdb_00004m2a

Crystal structure of the udp-glucose pyrophosphorylase from Leishmania major in the post-reactive state

• PDB DOI: https://doi.org/10.2210/pdb4M2A/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-05 Released: 2014-01-29 
• Deposition Author(s): Fuehring, J., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.250 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Catalytic Mechanism and Allosteric Regulation of Udp-Glucose Pyrophosphorylase from Leishmania Major

Fuehring, J., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

(2013) ACS Catal 3: 2161-2985

• DOI: https://doi.org/10.1021/cs4007777

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 56.74 kDa 
• Atom Count: 4,433 
• Modeled Residue Count: 483 
• Deposited Residue Count: 505 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose pyrophosphorylase	A	505	Leishmania major	Mutation(s): 0  Gene Names: LMJF_18_0990, UGP EC: 2.7.7.9
UniProt
Find proteins for Q4QDU3 (Leishmania major) Explore Q4QDU3  Go to UniProtKB:  Q4QDU3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.250 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.79	α = 90
b = 89.09	β = 90
c = 136.49	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
CNS	refinement
XDS	data reduction
SADABS	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Fuehring, J., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description