5KHA | pdb_00005kha

Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)

• PDB DOI: https://doi.org/10.2210/pdb5KHA/pdb

• Classification: LIGASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-14 Released: 2016-07-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)

Abendroth, J., Delker, S.L., Lorimer, D.D., Edwards, T.E.

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: 124.06 kDa 
• Atom Count: 8,854 
• Modeled Residue Count: 1,052 
• Deposited Residue Count: 1,098 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine-dependent NAD+ synthetase	A, B	549	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  nadE, A7A43_14755, AB895_2341, AB988_2173, ABUW_3069, ACX60_14085, APD31_16600, AQ480_16865, IOMTU433_2979, IX87_01870, TE32_15345 EC: 6.3.5.1 (PDB Primary Data), 6.3.1.5 (PDB Primary Data)
UniProt
Find proteins for V5VHL3 (Acinetobacter baumannii) Explore V5VHL3  Go to UniProtKB:  V5VHL3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EDO	D [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35KHA

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.88	α = 90
b = 123.75	β = 110.93
c = 73.65	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
PHENIX	model building
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2016-11-09
  Changes: Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description