3Q4G | pdb_00003q4g

Structure of NAD synthetase from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb3Q4G/pdb

• Classification: LIGASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-12-23 Released: 2011-01-26 
• Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Structure of NAD synthetase from Vibrio cholerae

Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., 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: 61.99 kDa 
• Atom Count: 4,521 
• Modeled Residue Count: 523 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A, B	279	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1  Gene Names: nadE, VCD_000045 EC: 6.3.1.5
UniProt
Find proteins for Q9KMW1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMW1  Go to UniProtKB:  Q9KMW1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.40 Å
• R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33q4g

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.426	α = 90
b = 93.426	β = 90
c = 165.297	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-10-08
  Changes: Database references
• Version 1.3: 2014-11-12
  Changes: Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary