5UU6

The crystal structure of nitroreductase A from Vibrio parahaemolyticus RIMD 2210633

• PDB DOI: https://doi.org/10.2210/pdb5UU6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-16 Released: 2017-03-01 
• Deposition Author(s): Tan, K., Zhou, M., 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: 1.95 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of nitroreductase A from Vibrio parahaemolyticus RIMD 2210633

Tan, K., Zhou, M., 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 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 110.3 kDa 
• Atom Count: 7,715 
• Modelled Residue Count: 937 
• Deposited Residue Count: 972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-flavin oxidoreductase	A, B, C, D	243	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VPA1601
UniProt
Find proteins for Q87FS7 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87FS7  Go to UniProtKB:  Q87FS7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
GOL	L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A], H [auth B], J [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.004	α = 90
b = 71.609	β = 93.15
c = 110.45	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: 2017-03-01 
Deposition Author(s): Tan, K., Zhou, M., 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: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection, Database references
• Version 1.5: 2024-11-06
  Changes: Structure summary