1CBN

ATOMIC RESOLUTION (0.83 ANGSTROMS) CRYSTAL STRUCTURE OF THE HYDROPHOBIC PROTEIN CRAMBIN AT 130 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Observed: 0.106 

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This is version 1.4 of the entry. See complete history


Literature

Atomic resolution (0.83 A) crystal structure of the hydrophobic protein crambin at 130 K.

Teeter, M.M.Roe, S.M.Heo, N.H.

(1993) J Mol Biol 230: 292-311

  • DOI: 10.1006/jmbi.1993.1143
  • Primary Citation of Related Structures:  
    1CBN

  • PubMed Abstract: 
  • To enhance the already high quality of diffraction data for crystals of the hydrophobic protein crambin, X-ray data were collected at 130 K by the method of H. Hope to 0.83 A resolution. Refinement with PROLSQ yields a model with an R value of 10.5%. The final model had three parameter anisotropic vibration factors for all atoms, which included 367 protein heavy atoms, 372 hydrogen atoms and 144 solvent atoms with one ethanol molecule ...

    To enhance the already high quality of diffraction data for crystals of the hydrophobic protein crambin, X-ray data were collected at 130 K by the method of H. Hope to 0.83 A resolution. Refinement with PROLSQ yields a model with an R value of 10.5%. The final model had three parameter anisotropic vibration factors for all atoms, which included 367 protein heavy atoms, 372 hydrogen atoms and 144 solvent atoms with one ethanol molecule. Dihedral angles and hydrogen-bonding distances generally agree with earlier studies of high-resolution protein structures, but some new patterns are noted. Solvent-related helix distortions are reminiscent of those described by others. Helix and beta-sheet regions show distinct patterns in their side-chain conformations. Despite crambin's hydrophobic nature, its accessible surface area in the crystal is surprisingly close to that of water-soluble proteins like myoglobin and carboxypeptidase A. More of crambin's hydrophobic surface is buried in the crystal, perhaps accounting for its high order of diffraction. A total of 24% of the 46 residues show discrete disorder at 130 K. This includes five side-chains at both 300 and 130 K, and six more side-chains and an ethanol molecule at 130 K. Disorder is associated with the sequence microheterogeneity at Pro/Ser22 and Leu/Ile25, with space filling or with solvent disorder. Correlated conformations extend over three to five residues. The patterns of disorder in this structure reveal important principles of protein structure and its dynamics. Finding disordered groups correlated over 5 to 8 A suggests that co-ordinated motion extends in groups rather than simply as uncorrelated movement around an atom center. Thermal diffuse scattering experiments on insulin and lysozyme are consistent with this interpretation. Nearly all of the protein-bound solvent has been located. Less than 1% of protein accessible surface area remains uncovered by solvent or crystal contacts. Preliminary analysis of the solvent network reveals two main networks in each of four solvent regions.


    Related Citations: 
    • Cryocrystallography of Biological Macromolecules: A Generally Applicable Method
      Hope, H.
      (1988) Acta Crystallogr B 44: 22
    • An Empirical Examination of Potential Energy Minimization Using the Well-Determined Structure of the Protein Crambin
      Whitlow, M., Teeter, M.M.
      (1986) J Am Chem Soc 108: 7163
    • Progress in the Water Structure of the Protein Crambin by X-Ray Diffraction at 140 K
      Teeter, M.M., Hope, H.
      (1986) Ann N Y Acad Sci 482: 163
    • Water Structure of a Hydrophobic Protein at Atomic Resolution. Pentagon Rings of Water Molecules in Crystals of Crambin
      Teeter, M.M.
      (1984) Proc Natl Acad Sci U S A 81: 6014
    • Structure of the Hydrophobic Protein Crambin Determined Directly from the Anomalous Scattering of Sulphur
      Hendrickson, W.A., Teeter, M.M.
      (1981) Nature 290: 107
    • Highly Ordered Crystals of the Plant Seed Protein Crambin
      Teeter, M.M., Hendrickson, W.A.
      (1979) J Mol Biol 127: 219

    Organizational Affiliation

    Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02167.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRAMBINA46Crambe hispanica subsp. abyssinicaMutation(s): 2 
Gene Names: THI2
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica)
Explore P01542 
Go to UniProtKB:  P01542
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EOH
Query on EOH

Download Ideal Coordinates CCD File 
B [auth A]ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Observed: 0.106 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.763α = 90
b = 18.492β = 90.61
c = 22.333γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2014-02-05
    Changes: Atomic model, Other
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other