3KO6 | pdb_00003ko6

Crystal structure of yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate

• PDB DOI: https://doi.org/10.2210/pdb3KO6/pdb

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


• Deposited: 2009-11-13 Released: 2010-11-17 
• Deposition Author(s): Ma, X.-X., Guo, P.-C., Chen, Y., Zhou, C.-Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal structure of yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate

Ma, X.-X., Guo, P.-C., Chen, Y., Zhou, C.-Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 39.84 kDa 
• Atom Count: 2,854 
• Modeled Residue Count: 352 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0067 GAF domain-containing protein YKL069W	A, B	180	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YKL069W EC: 1.8.4.14
UniProt
Find proteins for P36088 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36088  Go to UniProtKB:  P36088

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SME	C [auth A], D [auth B]	METHIONINE SULFOXIDE C5 H11 N O3 S QEFRNWWLZKMPFJ-ZXPFJRLXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.548	α = 90
b = 73.548	β = 90
c = 163.56	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Ma, X.-X., Guo, P.-C., Chen, Y., Zhou, C.-Z.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary