5DUL | pdb_00005dul

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb5DUL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-18 Released: 2015-09-30 
• Deposition Author(s): Osipiuk, J., Mulligan, R., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis in complex with NADPH .

Osipiuk, J., Mulligan, R., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 176.7 kDa 
• Atom Count: 11,690 
• Modeled Residue Count: 1,519 
• Deposited Residue Count: 1,604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B, C, D	401	Yersinia pestis	Mutation(s): 0  Gene Names: dxr, YPO1048, y3131, YP_2802 EC: 1.1.1.267
UniProt
Find proteins for Q8ZH62 (Yersinia pestis) Explore Q8ZH62  Go to UniProtKB:  Q8ZH62

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], F [auth B], G [auth C], H [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35dul

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.306	α = 90
b = 121.306	β = 90
c = 86.827	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-30 
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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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272200700058C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description