4XPD | pdb_00004xpd

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

• PDB DOI: https://doi.org/10.2210/pdb4XPD/pdb

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


• Deposited: 2015-01-16 Released: 2016-07-20 
• Deposition Author(s): Dong, J., Wang, S., York, J.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.297 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) 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: 149.74 kDa 
• Atom Count: 9,262 
• Modelled Residue Count: 1,122 
• 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
human ACTH8	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
G4P	E [auth A]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.297 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.564	α = 90
b = 113.649	β = 90
c = 146.721	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary