9BIV

Crystal Structure of Ubc13 with a New Active Site Loop Conformation

• PDB DOI: https://doi.org/10.2210/pdb9BIV/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-24 Released: 2024-05-08 
• Deposition Author(s): Farraj, R.A., Edwards, R.A., Glover, J.N.M.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.177 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

Crystal Structure of Ubc13 with a New Active Site Loop Conformation

Farraj, R.A., Edwards, R.A., Glover, J.N.M.

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)

Macromolecule Content

• Total Structure Weight: 33.54 kDa 
• Atom Count: 2,735 
• Modelled Residue Count: 288 
• Deposited Residue Count: 297 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 variant 2	A	145	Homo sapiens	Mutation(s): 0  Gene Names: UBE2V2, MMS2, UEV2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15819 (Homo sapiens) Explore Q15819  Go to UniProtKB:  Q15819
PHAROS:  Q15819 GTEx:  ENSG00000169139

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	B	152	Homo sapiens	Mutation(s): 0  Gene Names: UBE2N, BLU EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
PHAROS:  P61088 GTEx:  ENSG00000177889

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.177 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.361	α = 90
b = 42.942	β = 108.37
c = 93.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Farraj, R.A., Edwards, R.A., Glover, J.N.M.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release