6I03 | pdb_00006i03

D10N variant of beta-phosphoglucomutase from Lactococcus lactis complexed with tetrafluoroaluminate and beta-G6P to 1.02 A

• PDB DOI: https://doi.org/10.2210/pdb6I03/pdb

• Classification: ISOMERASE
• Organism(s): Lactococcus lactis subsp. lactis Il1403
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-10-24 Released: 2019-11-20 
• Deposition Author(s): Robertson, A.J., Waltho, J.P.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.175 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Proton transfer modulates the electrostatic environment in a general acid-base catalyzed phosphoryl transfer reaction

Robertson, A.J., Bisson, C., Waltho, J.P.

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)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 24.68 kDa 
• Atom Count: 2,216 
• Modeled Residue Count: 220 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase	A	222	Lactococcus lactis subsp. lactis Il1403	Mutation(s): 4  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BG6 (Subject of Investigation/LOI)	C [auth A]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
ALF (Subject of Investigation/LOI)	B [auth A]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.175 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.52	α = 90
b = 54.28	β = 90
c = 104.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Robertson, A.J., Waltho, J.P.

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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: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-20
  Changes: Structure summary