1A2P

BARNASE WILDTYPE STRUCTURE AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Observed: 0.111 

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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 D Biol Crystallogr 55: 386-398

  • DOI: 10.1107/s0907444998010865
  • Primary Citation of Related Structures:  
    1A2P

  • 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 anisotropic atomic displacement parameters resulted in increased accuracy of the structure ...

    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 Châtenay-Malabry CEDEX, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BARNASEA, B, C110Bacillus amyloliquefaciensMutation(s): 0 
EC: 3.1.27
UniProt
Find proteins for P00648 (Bacillus amyloliquefaciens)
Explore P00648 
Go to UniProtKB:  P00648
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Observed: 0.111 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.97α = 90
b = 58.97β = 90
c = 81.58γ = 120
Software Package:
Software NamePurpose
SHELXL-93model building
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
SHELXL-93phasing
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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