5V0R | pdb_00005v0r

Crystal structure of ubiquitin-conjugating enzyme from Naegleria fowleri with modified Cys99

• PDB DOI: https://doi.org/10.2210/pdb5V0R/pdb

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


• Deposited: 2017-02-28 Released: 2017-03-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Crystal structure of ubiquitin-conjugating enzyme from Naegleria fowleri with modified Cys99

Irwin, R.M., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.46 kDa 
• Atom Count: 1,416 
• Modeled Residue Count: 146 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme	A	169	Naegleria fowleri	Mutation(s): 0
UniProt
Find proteins for A0A1W2VMZ9 (Naegleria fowleri) Explore A0A1W2VMZ9  Go to UniProtKB:  A0A1W2VMZ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSA	A	L-PEPTIDE LINKING	C6 H11 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35V0R

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.36	α = 90
b = 85.24	β = 90
c = 33.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary