5OK0 | pdb_00005ok0

Structure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis trapped with native reaction intermediate beta-glucose 1,6-bisphosphate to 2.2A resolution.

• PDB DOI: https://doi.org/10.2210/pdb5OK0/pdb

• Classification: ISOMERASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-07-25 Released: 2018-08-29 
• Deposition Author(s): Robertson, A.J., Bisson, C.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.292 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture

Johnson, L.A., Robertson, A.J., Baxter, N.J., Trevitt, C.R., Bisson, C., Jin, Y., Wood, H.P., Hounslow, A.M., Cliff, M.J., Blackburn, G.M., Bowler, M.W., Waltho, J.P.

(2018) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.8b01612

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 24.29 kDa 
• Atom Count: 1,790 
• Modeled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase	A	218	Lactococcus lactis	Mutation(s): 3  Gene Names: pgmB, LL0429, L0001 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
B16 (Subject of Investigation/LOI)	B [auth A]	1,6-di-O-phosphono-beta-D-glucopyranose C6 H14 O12 P2 RWHOZGRAXYWRNX-DVKNGEFBSA-N
PDO	D [auth A]	1,3-PROPANDIOL C3 H8 O2 YPFDHNVEDLHUCE-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.292 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.81	α = 90
b = 54.94	β = 90
c = 103.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
xia2	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Robertson, A.J., Bisson, C.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M021637/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K016245/1

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary