6MJ9 | pdb_00006mj9

CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME FROM NAEGLERIA FOWLERI, APO FORM

• PDB DOI: https://doi.org/10.2210/pdb6MJ9/pdb

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


• Deposited: 2018-09-20 Released: 2018-10-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME FROM NAEGLERIA FOWLERI, APO FORM

Davies, D.R., Dranow, D.M., Abendroth, J., Lorimer, D.D., 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: 19.34 kDa 
• Atom Count: 1,230 
• Modeled Residue Count: 145 
• 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36mj9

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.3	α = 90
b = 42.87	β = 90
c = 89.96	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description