7XHS | pdb_00007xhs

Crystal structure of CipA crystal produced by cell-free protein synthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7XHS

This is version 1.1 of the entry. See complete history

Literature

Cell-free protein crystallization for nanocrystal structure determination.

Abe, S.Tanaka, J.Kojima, M.Kanamaru, S.Hirata, K.Yamashita, K.Kobayashi, A.Ueno, T.

(2022) Sci Rep 12: 16031-16031

  • DOI: https://doi.org/10.1038/s41598-022-19681-9
  • Primary Citation Related Structures: 
    7XHR, 7XHS, 7XWS

  • PubMed Abstract: 

    In-cell protein crystallization (ICPC) has been investigated as a technique to support the advancement of structural biology because it does not require protein purification and a complicated crystallization process. However, only a few protein structures have been reported because these crystals formed incidentally in living cells and are insufficient in size and quality for structure analysis. Here, we have developed a cell-free protein crystallization (CFPC) method, which involves direct protein crystallization using cell-free protein synthesis. We have succeeded in crystallization and structure determination of nano-sized polyhedra crystal (PhC) at a high resolution of 1.80 Å. Furthermore, nanocrystals were synthesized at a reaction scale of only 20 μL using the dialysis method, enabling structural analysis at a resolution of 1.95 Å. To further demonstrate the potential of CFPC, we attempted to determine the structure of crystalline inclusion protein A (CipA), whose structure had not yet been determined. We added chemical reagents as a twinning inhibitor to the CFPC solution, which enabled us to determine the structure of CipA at 2.11 Å resolution. This technology greatly expands the high-throughput structure determination method of unstable, low-yield, fusion, and substrate-biding proteins that have been difficult to analyze with conventional methods.


  • Organizational Affiliation
    • School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan. saabe@bio.titech.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 11.73 kDa 
  • Atom Count: 738 
  • Modeled Residue Count: 93 
  • Deposited Residue Count: 104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cro/Cl family transcriptional regulator104PhotorhabdusMutation(s): 0 
Gene Names: C6H68_06435
UniProt
Find proteins for Q7N6H4 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Explore Q7N6H4 
Go to UniProtKB:  Q7N6H4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7N6H4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.09α = 90
b = 61.09β = 90
c = 54.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Cootmodel building
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18H05421
Japan Society for the Promotion of Science (JSPS)JapanJP19H02830
Japan Science and TechnologyJapanJPMJTR20U1

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection