3D8P | pdb_00003d8p

Crystal structure of acetyltransferase of GNAT family (NP_373092.1) from STAPHYLOCOCCUS AUREUS MU50 at 2.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3D8P/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-23 Released: 2008-10-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of acetyltransferase of GNAT family (NP_373092.1) from STAPHYLOCOCCUS AUREUS MU50 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.55 kDa 
• Atom Count: 2,926 
• Modeled Residue Count: 318 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acetyltransferase of GNAT family	A, B	163	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: NP_373092.1, SAV2568
UniProt
Find proteins for A0A0H3JTS0 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JTS0  Go to UniProtKB:  A0A0H3JTS0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	D [auth A], E [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33D8P

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.597	α = 90
b = 135.597	β = 90
c = 103.578	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary
• Version 1.6: 2025-10-22
  Changes: Structure summary