5DB4 | pdb_00005db4

Mycobacterium abscessus NadD in complex with Mg-ATP, space group I41

• PDB DOI: https://doi.org/10.2210/pdb5DB4/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacteroides abscessus ATCC 19977
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-20 Released: 2016-08-24 
• Deposition Author(s): Reed, R.W., Korotkov, K.V., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Mycobacterium abscessus NadD in complex with Mg-ATP, space group I41

Reed, R.W., Korotkov, K.V.

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.08 kDa 
• Atom Count: 2,942 
• Modeled Residue Count: 354 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate-nucleotide adenylyltransferase	A, B	216	Mycobacteroides abscessus ATCC 19977	Mutation(s): 0  Gene Names: nadD, MAB_1621 EC: 2.7.7.18
UniProt
Find proteins for B1MMZ4 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)) Explore B1MMZ4  Go to UniProtKB:  B1MMZ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A], E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.098	α = 90
b = 67.098	β = 90
c = 229.538	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Reed, R.W., Korotkov, K.V., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R03AI117361
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103486
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description