5EJF | pdb_00005ejf

Crystal structure of NAD kinase P101A mutant from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb5EJF/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-01 Released: 2016-11-09 
• Deposition Author(s): Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NAD kinase 1 from Listeria monocytogenes: P101A mutant

Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.08 kDa 
• Atom Count: 8,378 
• Modeled Residue Count: 1,008 
• Deposited Residue Count: 1,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD kinase 1	A, B, C, D	272	Listeria monocytogenes	Mutation(s): 0  Gene Names: nadK1, lmo0968 EC: 2.7.1.23
UniProt
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8D7  Go to UniProtKB:  Q8Y8D7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.042	α = 90
b = 119.174	β = 100.98
c = 67.593	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Poncet-Montange, G., Assairi, L., Gelin, M., Pochet, S., Labesse, G.

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Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description