5OJW | pdb_00005ojw

S. cerevisiae UBC13 - MMs2 complex

• PDB DOI: https://doi.org/10.2210/pdb5OJW/pdb

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


• Deposited: 2017-07-24 Released: 2017-08-02 
• Deposition Author(s): Sharon, I., Rathi, R., Levin-Kravets, O., Attali, I., Prag, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.205 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

S. cerevisiae UBC13 - MMs2 complex

Sharon, I., Rathi, R., Levin-Kravets, O., Attali, I., Prag, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.93 kDa 
• Atom Count: 2,693 
• Modeled Residue Count: 289 
• Deposited Residue Count: 289 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 13	A	152	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: UBC13, YDR092W, YD6652.04 EC: 2.3.2.23
UniProt
Find proteins for P52490 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52490  Go to UniProtKB:  P52490

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme variant MMS2	B	137	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: MMS2, YGL087C
UniProt
Find proteins for P53152 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53152  Go to UniProtKB:  P53152

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.205 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.425	α = 90
b = 66.281	β = 90
c = 126.614	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Sharon, I., Rathi, R., Levin-Kravets, O., Attali, I., Prag, G.

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description