6HDF | pdb_00006hdf

D170N variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 1.4 A.

• PDB DOI: https://doi.org/10.2210/pdb6HDF/pdb

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


• Deposited: 2018-08-17 Released: 2020-08-26 
• Deposition Author(s): Wood, H.P., Robertson, A.J., Bisson, C., Waltho, J.P.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Transition state of phospho-enzyme hydrolysis in beta-phosphoglucomutase.

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.

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.14 kDa 
• Atom Count: 3,771 
• Modeled Residue Count: 438 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase	A, B	221	Lactococcus lactis subsp. lactis Il1403	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	H [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.77	α = 90
b = 119.31	β = 94.8
c = 53.17	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: 2020-08-26 
Deposition Author(s): Wood, H.P., Robertson, A.J., Bisson, C., Waltho, J.P.

---

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: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description