5EMZ | pdb_00005emz

Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit

• PDB DOI: https://doi.org/10.2210/pdb5EMZ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-11-07 Released: 2016-11-16 
• Deposition Author(s): Nakasone, M.A., Paukstelis, P.J., Fushman, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Structural characterization and practical fluorescence applications of the F45W ubiquitin mutant

Nakasone, M.A., Geng, C., Chojnacki, M., Glickman, M., Paukstelis, P.J., Fushman, D.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.05 kDa 
• Atom Count: 4,161 
• Modeled Residue Count: 448 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A, C, E	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B, D, F	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth B], H [auth D], I [auth E], J [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.87	α = 90
b = 78.92	β = 97.93
c = 91.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Nakasone, M.A., Paukstelis, P.J., Fushman, D.

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary