3HMQ | pdb_00003hmq

1.9 Angstrom resolution crystal structure of a NAD synthetase (nadE) from Salmonella typhimurium LT2 in complex with NAD(+)

• PDB DOI: https://doi.org/10.2210/pdb3HMQ/pdb

• Classification: LIGASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-29 Released: 2009-06-16 
• Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., 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: 1.90 Å
• R-Value Free: 
  0.187 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.144 (Depositor) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

1.9 Angstrom resolution crystal structure of a NAD synthetase (nadE) from Salmonella typhimurium LT2 in complex with NAD(+)

Halavaty, A.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., 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)

Macromolecule Content 

• Total Structure Weight: 32.14 kDa 
• Atom Count: 2,718 
• Modeled Residue Count: 262 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A	275	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: nadE, STM1310 EC: 6.3.1.5
UniProt
Find proteins for Q8ZPU5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPU5  Go to UniProtKB:  Q8ZPU5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	J [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.187 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.144 (Depositor) 
• R-Value Observed: 0.146 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33hmq

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.82	α = 90
b = 91.82	β = 90
c = 75.05	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
XDS	data scaling
Structure	phasing
SHELXD	phasing
SHELXE	model building
Bp3	phasing
SOLOMON	phasing
ARP	model building
WARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-12-07
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Database references
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary