4HNX | pdb_00004hnx

The NatA Acetyltransferase Complex Bound To ppGpp

• PDB DOI: https://doi.org/10.2210/pdb4HNX/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-21 Released: 2014-03-26 
• Deposition Author(s): Neubauer, J.L., Immormino, R.M., Dollins, D.E., Endo-Streeter, S.T., Pemble IV, C.W., York, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.213 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

The Protein Complex NatA Binds Inositol Hexakisphosphate and Exhibits Conformational Flexibility

Neubauer, J.L., Pham, T., Immormino, R.M., Dollins, D.E., Endo-Streeter, S.T., Li, S., Pemble IV, C.W., York, J.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 129.56 kDa 
• Atom Count: 7,408 
• Modeled Residue Count: 926 
• Deposited Residue Count: 1,111 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex subunit NAT1	A	863	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NAT1, AAA1, YDL040C, D2720
UniProt
Find proteins for P12945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12945  Go to UniProtKB:  P12945

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex catalytic subunit ARD1	B	248	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ARD1, YHR013C EC: 2.3.1.88 (PDB Primary Data), 2.3.1.255 (UniProt)
UniProt
Find proteins for P07347 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07347  Go to UniProtKB:  P07347

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P	C [auth A]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.213 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.105	α = 90
b = 137.105	β = 90
c = 179.603	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Neubauer, J.L., Immormino, R.M., Dollins, D.E., Endo-Streeter, S.T., Pemble IV, C.W., York, J.D.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Structure summary