5VIR | pdb_00005vir

Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abscessus in complex with NADP and compound FOL0091

• PDB DOI: https://doi.org/10.2210/pdb5VIR/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacteroides abscessus ATCC 19977
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-17 Released: 2017-04-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abcesus in complex with NADP and compound FOL0091

Abendroth, J., Davies, D.R., Korotkov, K.V., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.86 kDa 
• Atom Count: 3,322 
• Modeled Residue Count: 377 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable nicotinate-nucleotide adenylyltransferase	A, B	233	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
NAP	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
9CG	C [auth A], E [auth B]	1H,3H-naphtho[1,8-cd]pyran-1-one C12 H8 O2 UKOVZLWSUZKTRL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VIR

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.38	α = 90
b = 116.11	β = 90
c = 55.52	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description