3IIE | pdb_00003iie

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis.

• PDB DOI: https://doi.org/10.2210/pdb3IIE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pseudotuberculosis YPIII
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-31 Released: 2009-08-11 
• Deposition Author(s): Osipiuk, J., Mulligan, R., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis.

Osipiuk, J., Mulligan, R., Stam, J., Anderson, W.F., Joachimiak, A.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87 kDa 
• Atom Count: 6,181 
• Modeled Residue Count: 779 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B	401	Yersinia pseudotuberculosis YPIII	Mutation(s): 0  Gene Names: dxr, YPK_1070 EC: 1.1.1.267
UniProt
Find proteins for B1JQG4 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII)) Explore B1JQG4  Go to UniProtKB:  B1JQG4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33iie

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.46	α = 90
b = 121.46	β = 90
c = 86.923	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Osipiuk, J., Mulligan, R., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description