5BY0 | pdb_00005by0

Crystal structure of magnesium-bound Duf89 protein Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb5BY0/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-09 Released: 2015-07-29 
• Deposition Author(s): Nocek, B., Cuff, M., Cui, H., Xu, X., Savchenko, A., Joachimiak, A., Yakunin, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Crystal structure of magnesium-bound Duf89 protein Saccharomyces cerevisiae

Nocek, B., Cuff, M., Cui, H., Xu, X., Savchenko, A., Joachimiak, A., Yakunin, A.

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: 54.75 kDa 
• Atom Count: 4,307 
• Modeled Residue Count: 465 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-glutamate O-methyltransferase	A	472	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YMR027W, YM9711.17 EC: 2.1.1 (PDB Primary Data), 3.1.3 (UniProt)
UniProt
Find proteins for Q04371 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04371  Go to UniProtKB:  Q04371

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.407	α = 90
b = 108.582	β = 97.04
c = 88.234	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Nocek, B., Cuff, M., Cui, H., Xu, X., Savchenko, A., Joachimiak, A., Yakunin, A.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Experimental preparation
• Version 2.0: 2024-11-20
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary