4EM6

The structure of Glucose-6-phosphate isomerase (GPI) from Brucella melitensis

• PDB DOI:  https://doi.org/10.2210/pdb4EM6/pdb

• Classification: ISOMERASE
• Organism(s): Brucella melitensis bv. 1 str. 16M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-11 Released: 2012-05-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.169 
• R-Value Work: 0.131 
• R-Value Observed: 0.133 

Literature

The structure of Glucose-6-phosphate isomerase (GPI) from Brucella melitensis

Clifton, M.C., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 240.78 kDa 
• Atom Count: 19,246 
• Modelled Residue Count: 2,182 
• Deposited Residue Count: 2,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate isomerase	A [auth D], B [auth A], C [auth B], D [auth C]	553	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0  Gene Names: pgi, BMEI1636 EC: 5.3.1.9
UniProt
Find proteins for Q8YF86 (Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)) Explore Q8YF86  Go to UniProtKB:  Q8YF86

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	N [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	F [auth D], G [auth A], K [auth B], M [auth B], P [auth C], Q [auth C], R [auth C], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth D], H [auth A], I [auth A], J [auth B], L [auth B], O [auth C], S [auth C], T [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.169 
• R-Value Work: 0.131 
• R-Value Observed: 0.133 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.59	α = 95.42
b = 72.73	β = 91.54
c = 115.25	γ = 110.06

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description