1XNG | pdb_00001xng

Crystal Structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb1XNG/pdb

• Classification: LIGASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-05 Released: 2005-04-05 
• Deposition Author(s): Kang, G.B., Kim, Y.S., Im, Y.J., Rho, S.H., Lee, J.H., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

Kang, G.B., Kim, Y.S., Im, Y.J., Rho, S.H., Lee, J.H., Eom, S.H.

(2005) Proteins 58: 985-988

• PubMed: 15645437 
• DOI: https://doi.org/10.1002/prot.20377
• Primary Citation of Related Structures:  
  1XNG, 1XNH

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Organizational Affiliation: 

Department of Life Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea.

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: 63.15 kDa 
• Atom Count: 4,457 
• Modelled Residue Count: 517 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A, B	268	Helicobacter pylori	Mutation(s): 0  EC: 6.3.1.5
UniProt
Find proteins for O25096 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25096  Go to UniProtKB:  O25096

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DND	D [auth A], G [auth B]	NICOTINIC ACID ADENINE DINUCLEOTIDE C21 H27 N6 O15 P2 SENPVEZBRZQVST-HISDBWNOSA-O
ATP	E [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.257 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.403	α = 90
b = 63.403	β = 90
c = 125.688	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-05 
Deposition Author(s): Kang, G.B., Kim, Y.S., Im, Y.J., Rho, S.H., Lee, J.H., Eom, S.H.

Revision History  

• Version 1.0: 2005-04-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations