4M83

Ensemble refinement of protein crystal structure (2IYF) of macrolide glycosyltransferases OleD complexed with UDP and Erythromycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2IYF - determined by Bolam, D.N., Roberts, S.M., Proctor, M.R., Turkenburg, J.P., Dodson, E.J., Martinez-Fleites, C., Yang, M., Davis, B.G., Davies, G.J., Gilbert, H.J.  

Literature

Crystal structure of macrolide glycosyltransferases OleD

Olmos, J.L.Jr.Wang, F.Martinez iii, E.Helmich, K.E.Singh, S.Xu, W.Bingman, C.A.Thorson, J.S.Phillips Jr., G.N.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oleandomycin glycosyltransferase
A, B
415Streptomyces antibioticusMutation(s): 0 
Gene Names: oleD (UGT102A2)
EC: 2.4.1.-
Find proteins for Q53685 (Streptomyces antibioticus)
Go to UniProtKB:  Q53685
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
ERY
Query on ERY

Download SDF File 
Download CCD File 
A, B
ERYTHROMYCIN A
C37 H67 N O13
ULGZDMOVFRHVEP-RWJQBGPGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.718α = 90.00
b = 65.778β = 100.42
c = 91.940γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary