4M83 | pdb_00004m83

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

• PDB DOI: https://doi.org/10.2210/pdb4M83/pdb

• Classification: Transferase/Antibiotic
• Organism(s): Streptomyces antibioticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-12 Released: 2013-09-11 
• Deposition Author(s): Wang, F., Helmich, K.E., Xu, W., Singh, S., Olmos Jr., J.L., Martinez iii, E., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.201 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 93.03 kDa 
• Atom Count: 6,648 
• Modeled Residue Count: 787 
• Deposited Residue Count: 830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oleandomycin glycosyltransferase	A, B	415	Streptomyces antibioticus	Mutation(s): 0  Gene Names: oleD EC: 2.4.1
UniProt
Find proteins for Q53685 (Streptomyces antibioticus) Explore Q53685  Go to UniProtKB:  Q53685

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ERY	C [auth A], E [auth B]	ERYTHROMYCIN A C37 H67 N O13 ULGZDMOVFRHVEP-RWJQBGPGSA-N
UDP	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.201 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.718	α = 90
b = 65.778	β = 100.42
c = 91.94	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Wang, F., Helmich, K.E., Xu, W., Singh, S., Olmos Jr., J.L., Martinez iii, E., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations