4L83 | pdb_00004l83

Structure of a putative Ubiquitin-conjugating enzyme E2 from Brugia malayi

• PDB DOI: https://doi.org/10.2210/pdb4L83/pdb

• Classification: LIGASE
• Organism(s): Brugia malayi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-15 Released: 2013-06-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.207 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Structure of a putative Ubiquitin-conjugating enzyme E2 from Brugia malayi

Clifton, M.C., Edwards, T.E.

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: 20.26 kDa 
• Atom Count: 1,627 
• Modeled Residue Count: 165 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ube2i2 protein	A	175	Brugia malayi	Mutation(s): 0  Gene Names: Bm1_40505

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.207 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34L83

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.85	α = 90
b = 52.03	β = 90
c = 108.61	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description