4EBK

Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, tobramycin-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.221 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TOYClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, tobramycin-bound

Stogios, P.J.Dong, A.Minasov, G.Evdokimova, E.Egorova, O.Yim, V.Kudritska, M.Courvalin, P.Savchenko, A.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside nucleotidyltransferase
A, B
272Pseudomonas aeruginosaMutation(s): 0 
Gene Names: ant(4')-IIb
UniProt
Find proteins for D0E7M2 (Pseudomonas aeruginosa)
Explore D0E7M2 
Go to UniProtKB:  D0E7M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0E7M2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TOY
Query on TOY

Download Ideal Coordinates CCD File 
C [auth A],
W [auth B]
TOBRAMYCIN
C18 H37 N5 O9
NLVFBUXFDBBNBW-PBSUHMDJSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth B]
FA [auth B]
GA [auth B]
HA [auth B]
IA [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
IYR
Query on IYR
A, B
L-PEPTIDE LINKINGC9 H10 I N O3TYR
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.221 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.906α = 90
b = 84.451β = 90
c = 98.762γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TOYClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-12-06
    Changes: Data collection
  • Version 1.3: 2024-11-06
    Changes: Structure summary