3DPI | pdb_00003dpi

Crystal Structure of NAD+ synthetase from Burkholderia Pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3DPI/pdb

• Classification: LIGASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-08 Released: 2008-07-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of NAD+ synthetase from Burkholderia Pseudomallei

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.08 kDa 
• Atom Count: 3,986 
• Modeled Residue Count: 499 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD+ synthetase	A, B	285	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: 76819159 EC: 6.3.1.5
UniProt
Find proteins for Q3JL79 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JL79  Go to UniProtKB:  Q3JL79

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.315	α = 90
b = 76.315	β = 90
c = 183.772	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description