1GOV

RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of Substrate-Free Microbial Ribonuclease Binase and of its Complexes with 3'Gmp and Sulfate Ions

Polyakov, K.M.Lebedev, A.A.Okorokov, A.L.Panov, K.I.Schulga, A.A.Pavlovsky, A.G.Karpeisky, M.Y.A.Dodson, G.G.

(2002) Acta Crystallogr.,Sect.D 58: 744

  • Primary Citation of Related Structures:  1GOU, 1GOY

  • PubMed Abstract: 
  • The structures of Bacillus intermedius ribonuclease (binase), an extracellular 109-residue enzyme, and its complexes with 3'GMP and sulfate ions were solved at 1.65 and 2.0 A, respectively. The structures were refined using REFMAC. The crystal of fre ...

    The structures of Bacillus intermedius ribonuclease (binase), an extracellular 109-residue enzyme, and its complexes with 3'GMP and sulfate ions were solved at 1.65 and 2.0 A, respectively. The structures were refined using REFMAC. The crystal of free binase belongs to the space group C2, whereas the crystals of complexes belong to the space group P2(1)2(1)2(1). In both crystal lattices the asymmetric unit contains two molecules which form an identical dimer. The structure of the dimer is such that only one of its subunits can bind the nucleotide in the 3'GMP-binase complex, where the guanyl base is located in the recognition loop of the enzyme. In both binase complex structures the phosphate group of 3'GMP or one of the sulfate ions make an electrostatic interaction with the binase molecule at the catalytic site. A second phosphate-binding site was found in the structures of the complexes at the cleft formed by the loop 34-39, the main chain of Arg82 and the side chain of Trp34. Comparison of the complex and unliganded enzyme crystal structures shows that there are some small but distinct differences in the specificity loop (56-62) and in the loops 34-39 and 99-104 associated with the binding of the nucleotide and sulfate ions.


    Related Citations: 
    • The Structural and Sequence Homology of Family of Microbial Ribonucleases
      Hill, C.,Dodson, G.,Heinemann, U.,Saenger, W.,Mitsui, Y.,Nakamura, K.,Borisov, S.,Tischenko, G.,Polyakov, K.,Pavlovsky, S.
      (1983) Trends Biochem.Sci. 8: 364
    • Three-Dimensional Structure of Ribonuclese from Balillus Intermedius 7P at 3A Resolution
      Pavlovsky, A.G.,Vagin, A.A.,Vainshtein, B.K.,Chepurnova, N.K.,Karpeisky, M.Y.
      (1983) FEBS Lett. 162: 167
    • Comparison of Active Sites of Some Microbial Ribonucleases: Structural Basis for Guanylic Specificity
      Sevcik, J.,Sanishvili, R.G.,Pavlovsky, A.G.,Polyakov, K.M.
      (1990) Trends Biochem.Sci. 15: 158


    Organizational Affiliation

    Institute of Crystallography, RAS, 107333 Moscow, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE
A, B
116Bacillus intermediusEC: 3.1.27.-
Find proteins for P00649 (Bacillus intermedius)
Go to UniProtKB:  P00649
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 111.380α = 90.00
b = 69.560β = 90.00
c = 33.460γ = 90.00
Software Package:
Software NamePurpose
BLANCphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance