4M60 | pdb_00004m60

Crystal structure of macrolide glycosyltransferases OleD

• PDB DOI: https://doi.org/10.2210/pdb4M60/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces antibioticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-08 Released: 2013-09-04 
• Deposition Author(s): Olmos Jr., J.L., Martinez III, E., Wang, F., Helmich, K.E., Singh, S., Xu, W., 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: 1.77 Å
• R-Value Free: 
  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of macrolide glycosyltransferases OleD

Olmos Jr., J.L., Martinez iii, E., Wang, F., 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)

Macromolecule Content 

• Total Structure Weight: 46.19 kDa 
• Atom Count: 3,175 
• Modeled Residue Count: 376 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oleandomycin glycosyltransferase	A	418	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.134	α = 90
b = 124.134	β = 90
c = 67.636	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHENIX	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Olmos Jr., J.L., Martinez III, E., Wang, F., Helmich, K.E., Singh, S., Xu, W., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary