1XNH | pdb_00001xnh

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

• PDB DOI: https://doi.org/10.2210/pdb1XNH/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: 2.30 Å
• R-Value Free: 
  0.295 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.282 (DCC) 
• R-Value Observed: 
  0.259 (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 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 30.38 kDa 
• Atom Count: 2,001 
• Modeled Residue Count: 251 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.295 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.282 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.83	α = 90
b = 48.32	β = 109.97
c = 64.2	γ = 90

Software Package:

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

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: Derived calculations, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references