1IOZ

Crystal Structure of the C-HA-RAS Protein Prepared by the Cell-Free Synthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Selenomethionine incorporation into a protein by cell-free synthesis

Kigawa, T.Yamaguchi-Nunokawa, E.Kodama, K.Matsuda, T.Yabuki, T.Matsuda, N.Ishitani, R.Nureki, O.Yokoyama, S.

(2001) J Struct Funct Genomics 2: 29-35

  • DOI: 10.1023/a:1013203532303
  • Primary Citation of Related Structures:  
    1IOZ

  • PubMed Abstract: 
  • Multi-wavelength anomalous diffraction phasing is especially useful for high-throughput structure determinations. Selenomethionine substituted proteins are commonly used for this purpose. However, the cytotoxicity of selenomethionine drastically reduces the efficiency of its incorporation in in vivo expression systems ...

    Multi-wavelength anomalous diffraction phasing is especially useful for high-throughput structure determinations. Selenomethionine substituted proteins are commonly used for this purpose. However, the cytotoxicity of selenomethionine drastically reduces the efficiency of its incorporation in in vivo expression systems. In the present study, an improved E. coli cell-free protein synthesis system was used to incorporate selenomethionine into a protein, so that highly efficient incorporation could be achieved. A milligram quantity of selenomethionine-containing Ras was obtained using the cell-free system with dialysis. The mass spectrometry analysis showed that more than 95% of the methionine residues were substituted with selenomethionine. The crystal of this protein grew under the same conditions and had the same unit cell constants as those of the native Ras protein. The three-dimensional structure of this protein, determined by multi-wavelength anomalous diffraction phasing, was almost the same as that of the Ras protein prepared by in vivo expression. Therefore, the cell-free synthesis system could become a powerful protein expression method for high-throughput structure determinations by X-ray crystallography.


    Organizational Affiliation

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSFORMING PROTEIN P21/H-RAS-1A171Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.244 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.645α = 90
b = 82.645β = 90
c = 102.794γ = 120
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-03
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance