5DAS | pdb_00005das

Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212, form 2

• PDB DOI: https://doi.org/10.2210/pdb5DAS/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-20 Released: 2016-08-24 
• Deposition Author(s): Korotkov, K.V.
• 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: 2.20 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212

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: 92.38 kDa 
• Atom Count: 6,210 
• Modeled Residue Count: 723 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate-nucleotide adenylyltransferase	A [auth B], B [auth C], C [auth D], D [auth A]	201	Mycobacterium tuberculosis H37Rv	Mutation(s): 2  Gene Names: nadD, Rv2421c, MTCY428.26 EC: 2.7.7.18
UniProt
Find proteins for P9WJJ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJJ5  Go to UniProtKB:  P9WJJ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth B], F [auth C], G [auth D], H [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.82	α = 90
b = 156.13	β = 90
c = 48.95	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): Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R03AI117361
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, Refinement description