5JRO | pdb_00005jro

The crystal structure of azoreductase from Yersinia pestis CO92 in its Apo form

• PDB DOI: https://doi.org/10.2210/pdb5JRO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-06 Released: 2016-06-15 
• Deposition Author(s): Tan, K., Gu, M., Kwon, K., 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: 2.54 Å
• R-Value Free: 
  0.249 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of azoreductase from Yersinia pestis CO92 in its Apo form

Tan, K., Gu, M., Kwon, K., 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)

Macromolecule Content 

• Total Structure Weight: 43.96 kDa 
• Atom Count: 2,784 
• Modeled Residue Count: 366 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-dependent NADH-azoreductase	A, B	204	Yersinia pestis CO92	Mutation(s): 0  Gene Names: azoR, YPO2323, y2010, YP_2110 EC: 1.7 (PDB Primary Data), 1.6.5 (UniProt), 1.7.1.17 (UniProt)
UniProt
Find proteins for Q8ZE60 (Yersinia pestis) Explore Q8ZE60  Go to UniProtKB:  Q8ZE60

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.249 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35jro

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.257	α = 90
b = 45.135	β = 112.84
c = 72.699	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Tan, K., Gu, M., Kwon, K., 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	HHSN272201200026C

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description