1A2P

BARNASE WILDTYPE STRUCTURE AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refinement and structural analysis of barnase at 1.5 A resolution.

Martin, C.Richard, V.Salem, M.Hartley, R.Mauguen, Y.

(1999) Acta Crystallogr.,Sect.D 55: 386-398


  • PubMed Abstract: 
  • The structure of Bacillus amyloliquefaciens ribonuclease (barnase), an extracellular 110-residue enzyme initially solved at 2.0 A resolution, has been refined at 1.5 A using synchrotron radiation and an imaging-plate scanner. Refinement with anisotro ...

    The structure of Bacillus amyloliquefaciens ribonuclease (barnase), an extracellular 110-residue enzyme initially solved at 2.0 A resolution, has been refined at 1.5 A using synchrotron radiation and an imaging-plate scanner. Refinement with anisotropic atomic displacement parameters resulted in increased accuracy of the structure. The final model has a crystallographic R factor of 11.5% and an Rfree of 17.4%. The three independent molecules in the asymmetric unit, referred to as A, B and C, allowed detailed analysis of this final model and meaningful comparison with structures of barnase complexed either with nucleotide inhibitors or with its natural intracellular inhibitor, barstar. The analysis of the overall solvent structure revealed a similar number of water molecules associated with each barnase molecule; among these were 16 equivalent buried solvent molecules, the locations of which are discussed in detail and classified on the basis of their structural role. The importance of the water molecules' contribution to the barnase-barstar interaction is also highlighted. The high accuracy of the present analysis revealed the presence of a Zn2+ ion mediating the contacts between pairs of symmetry-related A, B or C molecules; such an ion had previously only been identified for pairs of C molecules.


    Organizational Affiliation

    Laboratoire de Physique, CNRS, ERS 582, Centre d'Etudes Pharmaceutiques, 92296 Ch√Ętenay-Malabry CEDEX, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BARNASE
A, B, C
110Bacillus 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 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 58.970α = 90.00
b = 58.970β = 90.00
c = 81.580γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHELXL-93phasing
X-PLORphasing
CCP4data scaling
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
SHELXL-93model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-04
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance