4YMI | pdb_00004ymi

Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abcessus in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb4YMI/pdb

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


• Deposited: 2015-03-06 Released: 2016-03-09 
• 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: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abcessus in complex with NADP

Abendroth, J., Dranow, D.M., Korotkov, K.V., Lorimer, D.D., Edwards, T.E.

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: 52.76 kDa 
• Atom Count: 3,334 
• Modeled Residue Count: 376 
• 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	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ADE	D [auth A], E [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34YMI

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.29	α = 90
b = 115.24	β = 90
c = 56.76	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description