4ZK7

Crystal structure of rescued two-component self-assembling tetrahedral cage T33-31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.

Bale, J.B.Park, R.U.Liu, Y.Gonen, S.Gonen, T.Cascio, D.King, N.P.Yeates, T.O.Baker, D.

(2015) Protein Sci 24: 1695-1701

  • DOI: 10.1002/pro.2748
  • Primary Citation of Related Structures:  
    4ZK7

  • PubMed Abstract: 
  • We recently reported the development of a computational method for the design of coassembling multicomponent protein nanomaterials. While four such materials were validated at high-resolution by X-ray crystallography, low yield of soluble protein prevented X-ray structure determination of a fifth designed material, T33-09 ...

    We recently reported the development of a computational method for the design of coassembling multicomponent protein nanomaterials. While four such materials were validated at high-resolution by X-ray crystallography, low yield of soluble protein prevented X-ray structure determination of a fifth designed material, T33-09. Here we report the design and crystal structure of T33-31, a variant of T33-09 with improved soluble yield resulting from redesign efforts focused on mutating solvent-exposed side chains to charged amino acids. The structure is found to match the computational design model with atomic-level accuracy, providing further validation of the design approach and demonstrating a simple and potentially general means of improving the yield of designed protein nanomaterials.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chorismate mutase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
130Thermus thermophilus HB8Mutation(s): 6 
Gene Names: TTHA0868
EC: 5.4.99.5
UniProt
Find proteins for Q5SJY4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJY4 
Go to UniProtKB:  Q5SJY4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Divalent-cation tolerance protein CutA
M, N, O, P, Q, R, S, T
M, N, O, P, Q, R, S, T, U, V, W, X
111Thermus thermophilus HB8Mutation(s): 13 
Gene Names: cutATTHA1356
UniProt
Find proteins for Q7SIA8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q7SIA8 
Go to UniProtKB:  Q7SIA8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.1α = 90
b = 128.4β = 90
c = 204.7γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations