5WP0

Crystal structure of NAD synthetase NadE from Vibrio fischeri

• PDB DOI: https://doi.org/10.2210/pdb5WP0/pdb

• Classification: LIGASE
• Organism(s): Aliivibrio fischeri ES114
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-03 Released: 2017-08-16 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Grimshaw, S., Savchenko, A., Anderson, W.F., 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: 0.261 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

Crystal structure of NAD synthetase NadE from Vibrio fischeri

Stogios, P.J.

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: 61.44 kDa 
• Atom Count: 4,328 
• Modelled Residue Count: 534 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A, B	279	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: nadE, VF_A0602 EC: 6.3.1.5
UniProt
Find proteins for Q5DZX4 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5DZX4  Go to UniProtKB:  Q5DZX4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.261 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M35WP0

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.252	α = 90
b = 115.887	β = 112.42
c = 55.086	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Grimshaw, S., Savchenko, A., Anderson, W.F., 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: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-09-27
  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