3K3V

Crystal structure the GYF domain of S. Cerevisiae SMY2

• PDB DOI: https://doi.org/10.2210/pdb3K3V/pdb

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


• Deposited: 2009-10-05 Released: 2010-05-19 
• Deposition Author(s): Ash, M.R., Faelber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.224 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

SMY2-type GYF domain recognition in mRNA surveillance complexes

Ash, M.R., Faelber, K., Kosslick, D., Albert, G., Roske, Y., Freund, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.11 kDa 
• Atom Count: 745 
• Modelled Residue Count: 79 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SMY2	A	100	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SMY2
UniProt
Find proteins for P32909 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32909  Go to UniProtKB:  P32909

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.224 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.220 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.4	α = 90
b = 68.4	β = 90
c = 111.321	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Ash, M.R., Faelber, K.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description