1JXX

CRAMBIN MIXED SEQUENCE FORM AT 200 K. PROTEIN/WATER SUBSTATES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

On the nature of a glassy state of matter in a hydrated protein: Relation to protein function.

Teeter, M.M.Yamano, A.Stec, B.Mohanty, U.

(2001) Proc Natl Acad Sci U S A 98: 11242-11247

  • DOI: https://doi.org/10.1073/pnas.201404398
  • Primary Citation of Related Structures:  
    1JXT, 1JXU, 1JXW, 1JXX, 1JXY

  • PubMed Abstract: 

    Diverse biochemical and biophysical experiments indicate that all proteins, regardless of size or origin, undergo a dynamic transition near 200 K. The cause of this shift in dynamic behavior, termed a "glass transition," and its relation to protein function are important open questions. One explanation postulated for the transition is solidification of correlated motions in proteins below the transition. We verified this conjecture by showing that crambin's radius of gyration (Rg) remains constant below approximately 180 K. We show that both atom position and dynamics of protein and solvent are physically coupled, leading to a novel cooperative state. This glassy state is identified by negative slopes of the Debye-Waller (B) factor vs. temperature. It is composed of multisubstate side chains and solvent. Based on generalization of Adam-Gibbs' notion of a cooperatively rearranging region and decrease of the total entropy with temperature, we calculate the slope of the Debye-Waller factor. The results are in accord with experiment.


  • Organizational Affiliation

    Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA. teeter@bc.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Crambin46Crambe hispanica subsp. abyssinicaMutation(s): 2 
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica)
Explore P01542 
Go to UniProtKB:  P01542
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01542
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EOH
Query on EOH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.87α = 90
b = 18.48β = 90.59
c = 22.37γ = 90
Software Package:
Software NamePurpose
LEHMANN-LARSENdata collection
TEXSANdata reduction
PROLSQrefinement
LEHMANN-LARSENdata reduction
TEXSANdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-31
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary