1PZV | pdb_00001pzv

Crystal structures of two UBC (E2) enzymes of the ubiquitin-conjugating system in Caenorhabditis elegans

• PDB DOI: https://doi.org/10.2210/pdb1PZV/pdb

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


• Deposited: 2003-07-14 Released: 2003-07-22 
• Deposition Author(s): Schormann, N., Lin, G., Li, S., Symersky, J., Qiu, S., Finley, J., Luo, D., Stanton, A., Carson, M., Luo, M., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.289 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of two UBC (E2) enzymes of the ubiquitin-conjugating system in Caenorhabditis elegans

Schormann, N., Lin, G., Li, S., Symersky, J., Qiu, S., Finley, J., Luo, D., Stanton, A., Carson, M., Luo, M., DeLucas, L., Pruett, P., Nagy, L., Arabashi, A., Gray, R., Johnson, D., Tsao, J., Bunzel, B., Huang, W., Shang, Q., Luan, C.-H., Lu, S., Zhang, J., McKinstry, A., Chen, H.

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: 18.96 kDa 
• Atom Count: 1,270 
• Modeled Residue Count: 152 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ubiquitin-conjugating enzyme E2-19 kDa	A	164	Caenorhabditis elegans	Mutation(s): 0  Gene Names: F58A4.10 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P34477 (Caenorhabditis elegans) Explore P34477  Go to UniProtKB:  P34477

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.289 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.474	α = 90
b = 52.184	β = 90
c = 68.882	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-22 
Deposition Author(s): Schormann, N., Lin, G., Li, S., Symersky, J., Qiu, S., Finley, J., Luo, D., Stanton, A., Carson, M., Luo, M., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2003-07-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Refinement description