3ZI4

The structure of Beta-phosphoglucomutase Inhibited With Glucose-6-phosphate and Scandium Tetrafluoride

• PDB DOI: https://doi.org/10.2210/pdb3ZI4/pdb

• Classification: ISOMERASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-01-03 Released: 2014-01-15 
• Deposition Author(s): Pellegrini, E., Bowler, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.174 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 

Literature

Metal Fluorides: Multi-Functional Tools for the Study of Phosphoryl Transfer Enzymes

Bowler, M.W., Pellegrini, E.

To be published.

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: 24.64 kDa 
• Atom Count: 2,134 
• Modelled Residue Count: 218 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-PHOSPHOGLUCOMUTASE	A	221	Lactococcus lactis	Mutation(s): 2  EC: 5.4.2.6
UniProt
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore P71447  Go to UniProtKB:  P71447

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BG6	C [auth A]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
SFL	D [auth A]	Scandium Tetrafluoride F4 Sc YVTFRTYUOUJWMQ-UHFFFAOYSA-J
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.174 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.152	α = 90
b = 54.238	β = 90
c = 104.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Pellegrini, E., Bowler, M.W.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Data collection
• Version 2.0: 2018-02-14
  Changes: Atomic model, Structure summary
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 2.2: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary