1BO4 | pdb_00001bo4

CRYSTAL STRUCTURE OF A GCN5-RELATED N-ACETYLTRANSFERASE: SERRATIA MARESCENS AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE

• PDB DOI: https://doi.org/10.2210/pdb1BO4/pdb

• Classification: TRANSFERASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-08-08 Released: 1998-10-07 
• Deposition Author(s): Wolf, E., Vassilev, A., Makino, Y., Sali, A., Nakatani, Y., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase.

Wolf, E., Vassilev, A., Makino, Y., Sali, A., Nakatani, Y., Burley, S.K.

(1998) Cell 94: 439-449

• PubMed: 9727487 
• DOI: https://doi.org/10.1016/s0092-8674(00)81585-8
• Primary Citation Related Structures: 
  1BO4


• PubMed Abstract: 
  

  The X-ray structure of a canonical GCN5-related N-acetyltransferase (GNAT), Serratia marcescens aminoglycoside 3-N-acetyltransferase, bound to coenzyme A (CoA) has been determined at 2.3 A resolution. The single domain alpha/beta protein resembles a cupped right hand wrapped around a cylinder and consists of a highly curved, six-stranded beta sheet of mixed polarity that is sandwiched between four alpha helices. The structure includes all four conserved GNAT motifs (C, D, A, and B) and represents the catalytic core of this large enzyme superfamily. Acetyl CoA recognition is mediated by a betaalpha structure derived from GNAT motif A, which presents an invariant Arg/Gln-X-X-Gly-X-Gly/Ala segment for hydrogen bonding with the cofactor. Motif B contributes acidic residues to the binding site for the positively charged antibiotic substrate.

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Organizational Affiliation: 
• Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 38.66 kDa 
• Atom Count: 2,475 
• Modeled Residue Count: 273 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)	A, B	168	Serratia marcescens	Mutation(s): 0  Gene Names: AACC1
UniProt
Find proteins for Q53396 (Serratia marcescens) Explore Q53396  Go to UniProtKB:  Q53396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	D [auth A], E [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SPD	C [auth A]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.54	α = 90
b = 102.26	β = 93.73
c = 50.14	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-07 
Deposition Author(s): Wolf, E., Vassilev, A., Makino, Y., Sali, A., Nakatani, Y., Burley, S.K.

Revision History  

• Version 1.0: 1998-10-07
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references