5VIX | pdb_00005vix

Crystal structure of Polyubiquitin with 3 ub domains, domains 1 and 2, from Naegleria fowleri ATCC 30863

• PDB DOI: https://doi.org/10.2210/pdb5VIX/pdb

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


• Deposited: 2017-04-17 Released: 2017-05-24 
• 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: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of polyubiquitin with 3 ub domains, domains 1 and 2, from Naegleria fowleri ATCC 30863

Abendroth, J., Mayclin, S.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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.42 kDa 
• Atom Count: 1,461 
• Modeled Residue Count: 154 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin	A	160	Naegleria fowleri	Mutation(s): 0
UniProt
Find proteins for D2V6G7 (Naegleria gruberi) Explore D2V6G7  Go to UniProtKB:  D2V6G7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	B [auth A], C [auth A], D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.02	α = 90
b = 67.71	β = 114.49
c = 35.83	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing
ARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection
• Version 1.2: 2019-07-03
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2020-06-17
  Changes: Atomic model, Data collection, Source and taxonomy
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description