Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 7.34 kDa 
• Atom Count: 520 
• Modelled Residue Count: 57 
• Deposited Residue Count: 62 
• Unique protein chains: 1

1QKW

Alpha-spectrin Src Homology 3 domain, N47G mutant in the distal loop.

• PDB DOI: 10.2210/pdb1QKW/pdb

• Classification: CYTOSKELETON
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1999-08-16 Released: 2000-08-18 
• Deposition Author(s): Vega, M.C., Martinez, J., Serrano, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the Ramachandran plot.

Vega, M.C., Martinez, J.C., Serrano, L.

(2000) Protein Sci 9: 2322-2328

• PubMed: 11206053 
• DOI: 10.1110/ps.9.12.2322
• Primary Citation of Related Structures:  
  1QKW, 1QKX


• PubMed Abstract: 
  

Residue Asn47 at position L1 of a type II' beta-turn of the alpha-spectrin SH3 domain is located in a disallowed region of the Ramachandran plot (phi = 56 +/- 12, psi = -118 +/- 17). Therefore, it is expected that replacement of Asn47 by Gly should result in a considerable stabilization of the protein. Thermodynamic analysis of the N47G and N47A mutants shows that the change in free energy is small (approximately 0.7 kcal/mol; approximately 3 kJ/mol) and comparable to that found when mutating a Gly to Ala in a alpha-helix or beta-sheet. X-ray structural analysis of these mutants shows that the conformation of the beta-turn does not change upon mutation and, therefore, that there is no relaxation of the structure, nor is there any gain or loss of interactions that could explain the small energy change. Our results indicate that the energetic definition of II' region of the Ramachandran plot (phi = 60 +/- 30, psi = -115 +/- 15) should be revised for at least Ala and Asn in structure validation and protein design.

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Organizational Affiliation: 

EMBL, Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA II SPECTRIN	A	62	Gallus gallus	Mutation(s): 1  Gene Names: SPTAN1, SPTA2
UniProt
Find proteins for P07751 (Gallus gallus) Explore P07751  Go to UniProtKB:  P07751

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.82	α = 90
b = 42.47	β = 90
c = 49.24	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-08-16 
• Released Date: 2000-08-18 
Deposition Author(s): Vega, M.C., Martinez, J., Serrano, L.

Revision History  

• Version 1.0: 2000-08-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Advisory, Data collection
• Version 1.4: 2019-10-09
  Changes: Data collection, Database references