5VVE

Crystal structure of phosphoglycerate mutase from Naegleria fowleri

• PDB DOI: https://doi.org/10.2210/pdb5VVE/pdb

• Classification: ISOMERASE
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-19 Released: 2017-08-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.195 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Crystal structure of phosphoglycerate mutase from Naegleria fowleri

Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 60.48 kDa 
• Atom Count: 4,725 
• Modelled Residue Count: 489 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase	A, B	258	Naegleria fowleri	Mutation(s): 0  Gene Names: NF0048460
UniProt
Find proteins for A0A2D0TCG6 (Naegleria fowleri) Explore A0A2D0TCG6  Go to UniProtKB:  A0A2D0TCG6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.195 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: I 2 2 2
• Diffraction Data: https://doi.org/10.18430/M35VVE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.61	α = 90
b = 89.33	β = 90
c = 157.88	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
PHENIX	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description