1STY

THE ALPHA ANEURISM: A STRUCTURAL MOTIF REVEALED IN AN INSERTION MUTANT OF STAPHYLOCOCCAL NUCLEASE

• PDB DOI: https://doi.org/10.2210/pdb1STY/pdb

• Classification: HYDROLASE (PHOSPHORIC DIESTER)
• Organism(s): Staphylococcus aureus
• Mutation(s): No 


• Deposited: 1993-02-18 Released: 1993-04-15 
• Deposition Author(s): Keefe, L.J., Lattman, E.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Work: 0.170 

Literature

The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease.

Keefe, L.J., Sondek, J., Shortle, D., Lattman, E.E.

(1993) Proc Natl Acad Sci U S A 90: 3275-3279

• PubMed: 8475069 
• DOI: https://doi.org/10.1073/pnas.90.8.3275
• Primary Citation of Related Structures:  
  1STY


• PubMed Abstract: 
  

  The x-ray crystal structure of a mutant of staphylococcal nuclease that contains a single glycine residue inserted in the C-terminal alpha-helix has been solved to 1.67 A resolution and refined to a crystallographic R value of 0.170. This inserted glycine residue is accommodated in the alpha-helix by formation of a previously uncharacterized bulge, which we term the alpha aneurism. A conformational search of known protein structures has identified the alpha aneurism in a number of protein families, including the histocompatibility antigens and hemoglobins.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.34 kDa 
• Atom Count: 1,278 
• Modelled Residue Count: 137 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STAPHYLOCOCCAL NUCLEASE	A	150	Staphylococcus aureus	Mutation(s): 0  EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus) Explore P00644  Go to UniProtKB:  P00644

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THP	C [auth A]	THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 CSNCBOPUCJOHLS-XLPZGREQSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Work: 0.170 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.952	α = 90
b = 46.952	β = 90
c = 62.895	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-04-15 
Deposition Author(s): Keefe, L.J., Lattman, E.E.

Revision History  

• Version 1.0: 1993-04-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.5: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.6: 2024-02-14
  Changes: Data collection, Database references, Derived calculations