3WE5 | pdb_00003we5

Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita

• PDB DOI: https://doi.org/10.2210/pdb3WE5/pdb

• Classification: LIGASE
• Organism(s): Cyclocybe aegerita
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-01 Released: 2014-07-09 
• Deposition Author(s): Li, D.F., Feng, L., Wang, D.C., Liu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita

Li, D.F., Feng, L., Wang, D.C., Liu, W.

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.48 kDa 
• Atom Count: 2,531 
• Modeled Residue Count: 282 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin conjugating enzyme	A, B	173	Cyclocybe aegerita	Mutation(s): 0  EC: 6.3.2.19
UniProt
Find proteins for H9CTH3 (Cyclocybe aegerita) Explore H9CTH3  Go to UniProtKB:  H9CTH3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.93	α = 90
b = 34.76	β = 108.88
c = 128.1	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Li, D.F., Feng, L., Wang, D.C., Liu, W.

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description