4ESE | pdb_00004ese

The crystal structure of azoreductase from Yersinia pestis CO92 in complex with FMN.

• PDB DOI: https://doi.org/10.2210/pdb4ESE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-23 Released: 2012-05-23 
• 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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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of acyl carrier protein phosphodiesterase from Yersinia pestis CO92 in complex with FMN.

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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.97 kDa 
• Atom Count: 1,805 
• Modeled Residue Count: 193 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-dependent NADH-azoreductase	A	204	Yersinia pestis CO92	Mutation(s): 0  Gene Names: azoR, y2010, YPO2323, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
12P	E [auth A]	DODECAETHYLENE GLYCOL C24 H50 O13 WRZXKWFJEFFURH-UHFFFAOYSA-N
FMN	B [auth A], C [auth A], D [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	G [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34ese

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.825	α = 90
b = 120.388	β = 90
c = 60.074	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Tan, K., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description