1JXT | pdb_00001jxt

CRAMBIN MIXED SEQUENCE FORM AT 160 K. PROTEIN/WATER SUBSTATES

• PDB DOI: https://doi.org/10.2210/pdb1JXT/pdb

• Classification: PLANT PROTEIN
• Organism(s): Crambe hispanica subsp. abyssinica
• Mutation(s): Yes 


• Deposited: 2001-09-08 Released: 2001-10-31 
• Deposition Author(s): Teeter, M.M., Yamano, A., Stec, B., Mohanty, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.89 Å
• R-Value Work: 
  0.145 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

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

• PubMed: 11572978 
• DOI: https://doi.org/10.1073/pnas.201404398
• Primary Citation 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.

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Organizational Affiliation: 
• Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.77 kDa 
• Atom Count: 419 
• Modeled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crambin	A	46	Crambe hispanica subsp. abyssinica	Mutation(s): 2
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica) Explore P01542  Go to UniProtKB:  P01542

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	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:  0.145 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.84	α = 90
b = 18.47	β = 90.8
c = 22.34	γ = 90

Software Package:

Software Name	Purpose
LEHMANN-LARSEN	data collection
TEXSAN	data reduction
MADSYS	phasing
PROLSQ	refinement
LEHMANN-LARSEN	data reduction
TEXSAN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-31 
Deposition Author(s): Teeter, M.M., Yamano, A., Stec, B., Mohanty, U.

Revision History  

• 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: 2024-10-30
  Changes: Structure summary