3P52 | pdb_00003p52

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

• PDB DOI: https://doi.org/10.2210/pdb3P52/pdb

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


• Deposited: 2010-10-07 Released: 2010-10-27 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Skarina, T., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.245 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Skarina, T., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.43 kDa 
• Atom Count: 3,659 
• Modeled Residue Count: 458 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A, B	249	Campylobacter jejuni	Mutation(s): 0  Gene Names: Cj0810, nadE EC: 6.3.1.5
UniProt
Find proteins for Q9PPB0 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB0  Go to UniProtKB:  Q9PPB0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	C [auth A], D [auth B], E [auth B], F [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.245 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33p52

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.945	α = 90
b = 120.945	β = 90
c = 91.795	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
CCP4	model building
MrBUMP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Skarina, T., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary