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RCSB PDB
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1,068,577 Computed Structure Models (CSM)
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 3N0S|pdb_00003n0s

Crystal structure of BA2930 mutant (H183A) in complex with AcCoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis.

Klimecka, M.M.Chruszcz, M.Font, J.Skarina, T.Shumilin, I.Onopryienko, O.Porebski, P.J.Cymborowski, M.Zimmerman, M.D.Hasseman, J.Glomski, I.J.Lebioda, L.Savchenko, A.Edwards, A.Minor, W.

(2011) J Mol Biology 410: 411-423

  • PubMed21601576 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1016/j.jmb.2011.04.076
  • Primary Citation of Related Structures:  
    3E4F,3IJW,3KZL,3N0M,3N0S

  • PubMed Abstract: 

    For the last decade, worldwide efforts for the treatment of anthrax infection have focused on developing effective vaccines. Patients that are already infected are still treated traditionally using different types of standard antimicrobial agents. The most popular are antibiotics such as tetracyclines and fluoroquinolones. While aminoglycosides appear to be less effective antimicrobial agents than other antibiotics, synthetic aminoglycosides have been shown to act as potent inhibitors of anthrax lethal factor and may have potential application as antitoxins. Here, we present a structural analysis of the BA2930 protein, a putative aminoglycoside acetyltransferase, which may be a component of the bacterium's aminoglycoside resistance mechanism. The determined structures revealed details of a fold characteristic only for one other protein structure in the Protein Data Bank, namely, YokD from Bacillus subtilis. Both BA2930 and YokD are members of the Antibiotic_NAT superfamily (PF02522). Sequential and structural analyses showed that residues conserved throughout the Antibiotic_NAT superfamily are responsible for the binding of the cofactor acetyl coenzyme A. The interaction of BA2930 with cofactors was characterized by both crystallographic and binding studies.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (ACO)


Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 


Find Similar Assemblies

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

Biological Assembly 2  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (ACO)


Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 


Find Similar Assemblies

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

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Macromolecule Content

  • Total Structure Weight: 124.61 kDa 
  • Atom Count: 8,881 
  • Modelled Residue Count: 1,060 
  • Deposited Residue Count: 1,072 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N3-acetyltransferaseA,
B [auth D],
C,
D [auth B]
268Bacillus anthracis str. AmesMutation(s): 1 
Gene Names: aacC7BA_2930GBAA2930GBAA_2930
EC: 2.3.1.81 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for A0A3P1UCA6 (Bacillus anthracis)
Explore A0A3P1UCA6 
Go to UniProtKB:  A0A3P1UCA6
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3P1UCA6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth D],
H [auth C],
I [auth B]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
K [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth D],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues 1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
B [auth D],
C,
D [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work: 0.173 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.036α = 90
b = 109.441β = 111.86
c = 74.048γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-03
    Changes: Database references
  • Version 1.3: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-22
    Changes: Data collection
  • Version 1.6: 2024-11-27
    Changes: Structure summary

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