8U5W | pdb_00008u5w

De novo designed pentameric helical bundle protein

• PDB DOI: https://doi.org/10.2210/pdb8U5W/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-13 Released: 2024-09-25 
• Deposition Author(s): Bick, M.J., Xu, C., Sankaran, B., Baker, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.279 (Depositor) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: in silico

Literature

De novo Design of Near Infrared Fluorescent Proteins

Xu, C., Liu, Y., Arus, B.A., Mishra, K., Bandi, V.G., Luciano, M.P., Kumar, A., Manton, J., Guo, Z., Bick, M.J., Xu, M., Zhang, K., Kang, A., De La Cruz, J., Brackenbrough, E., Gerben, S.R., Bera, A.K., Vaughan, J.C., Derivery, E., Schnermann, M.J., Stiel, A.C., Bruns, O., Baker, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content 

• Total Structure Weight: 89.67 kDa 
• Atom Count: 4,456 
• Modeled Residue Count: 670 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WSHC5	A, B, C, D, E, F, G, H, I, J	74	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.279 (Depositor) 
• R-Value Work:  0.234 (Depositor) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.588	α = 90
b = 74.353	β = 90
c = 194.338	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Bick, M.J., Xu, C., Sankaran, B., Baker, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release