1Z3D | pdb_00001z3d

Protein crystal growth improvement leading to the 2.5A crystallographic structure of ubiquitin-conjugating enzyme (ubc-1) from Caenorhabditis elegans

• PDB DOI: https://doi.org/10.2210/pdb1Z3D/pdb

• Classification: LIGASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-03-11 Released: 2005-03-22 
• Deposition Author(s): Gavira, J.A., DiGiammarino, E., Tempel, W., Toh, D., Liu, Z.J., Wang, B.C., Meehan, E., Ng, J.D., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Protein crystal growth improvement leading to the 2.5A crystallographic structure of ubiquitin-conjugating enzyme (ubc-1) from Caenorhabditis elegans

Gavira, J.A., DiGiammarino, E., Tempel, W., Toh, D., Liu, Z.J., Wang, B.C., Meehan, E., Ng, J.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.95 kDa 
• Atom Count: 1,241 
• Modeled Residue Count: 151 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 1	A	157	Caenorhabditis elegans	Mutation(s): 0  Gene Names: ubc-1 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P52478 (Caenorhabditis elegans) Explore P52478  Go to UniProtKB:  P52478

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.55	α = 90
b = 100.55	β = 90
c = 35.84	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-22 
Deposition Author(s): Gavira, J.A., DiGiammarino, E., Tempel, W., Toh, D., Liu, Z.J., Wang, B.C., Meehan, E., Ng, J.D., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Experimental preparation, Refinement description