1BRG

CRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic analysis of Phe-->Leu substitution in the hydrophobic core of barnase.

Chen, Y.W.Fersht, A.R.Henrick, K.

(1995) Acta Crystallogr.,Sect.D 51: 220-231

  • DOI: 10.1107/S0907444994008851

  • PubMed Abstract: 
  • The crystal structure of a barnase mutant, Phe-->Leu7 has been determined to 2.2 A resolution. No structural rearrangement is observed near the mutated residue. The F7L mutation is highly destabilizing and this is caused by the loss of extensive van ...

    The crystal structure of a barnase mutant, Phe-->Leu7 has been determined to 2.2 A resolution. No structural rearrangement is observed near the mutated residue. The F7L mutation is highly destabilizing and this is caused by the loss of extensive van der Waals contacts that wild-type Phe7 made with its neighbouring residues, and the exposure of a large hydrophobic pocket on the surface of the protein. The side-chain conformations of the mutated Leu7 residue have torsion angles chi(1) ranging from -138 degrees to -168 degrees and chi(2) ranging from +16 degrees to +70 degrees, for the three molecules in the asymmetric unit. These angles do not agree with the most frequently observed conformations in the protein side-chain rotamer library [Ponder & Richards (1987). J. Mol. Biol. 193, 775-791]. However, when compared to a more recent 'backbone-dependent' rotamer library [Dunbrack & Karplus (1993). J. Mol. Biol. 230, 543-574], the side-chain conformation of Leu7 agrees well with that of the most frequently observed rotamers. The side-chain conformation of Leu7 was found to be dictated by two factors: it has the lowest conformational energy and it buries the most hydrophobic surface area.


    Related Citations: 
    • Molecular Structures of a New Family of Ribonucleases
      Mauguen, Y.,Hartley, R.W.,Dodson, E.J.,Dodson, G.G.,Bricogne, G.,Chothia, C.,Jack, A.
      (1982) Nature 297: 162
    • Contribution of Hydrophobic Interactions to Protein Stability
      Kellis Junior, J.T.,Nyberg, K.,Sali, D.,Fersht, A.R.
      (1988) Nature 333: 784


    Organizational Affiliation

    Centre for Protein Engineering, Medical Research Council Centre, Cambridge, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BARNASE
A, B, C
108Bacillus amyloliquefaciensEC: 3.1.27.-
Find proteins for P00648 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P00648
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.168 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 58.723α = 90.00
b = 58.723β = 90.00
c = 82.026γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-04
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other