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: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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


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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oleandomycin glycosyltransferaseAB415Streptomyces antibioticusMutation(s): 0 
Gene Names: oleDUGT102A2
EC: 2.4.1
Find proteins for Q53685 (Streptomyces antibioticus)
Explore Q53685 
Go to UniProtKB:  Q53685
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERY
Query on ERY

Download CCD File 
A, B
ERYTHROMYCIN A
C37 H67 N O13
ULGZDMOVFRHVEP-RWJQBGPGSA-N
 Ligand Interaction
UDP
Query on UDP

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

Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.718α = 90
b = 65.778β = 100.42
c = 91.94γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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