4XNH | pdb_00004xnh

Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate

• PDB DOI: https://doi.org/10.2210/pdb4XNH/pdb

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


• Deposited: 2015-01-15 Released: 2016-07-20 
• Deposition Author(s): Dong, J., Wang, S., York, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate

Dong, J., Wang, S., York, J.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 149.79 kDa 
• Atom Count: 10,132 
• Modeled Residue Count: 1,148 
• Deposited Residue Count: 1,276 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex subunit NAT1	A	854	Saccharomyces cerevisiae	Mutation(s): 0
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	238	Saccharomyces cerevisiae	Mutation(s): 0  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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex subunit NAT5	C	176	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.3.1 (PDB Primary Data), 2.3.1.258 (UniProt)
UniProt
Find proteins for Q08689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08689  Go to UniProtKB:  Q08689

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYH8	D [auth F]	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01189 (Homo sapiens) Explore P01189  Go to UniProtKB:  P01189
PHAROS:  P01189 GTEx:  ENSG00000115138

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMC	G [auth F]	CARBOXYMETHYL COENZYME *A C23 H38 N7 O18 P3 S OBUOSIHPWVNVJN-GRFIIANRSA-N
ACO	F [auth C]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
IHP	E [auth A]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.475	α = 90
b = 114.515	β = 90
c = 146.978	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Dong, J., Wang, S., York, J.D.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 2.0: 2020-10-14
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references