1RGH

HYDROLASE, GUANYLORIBONUCLEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ribonuclease from Streptomyces aureofaciens at atomic resolution.

Sevcik, J.Dauter, Z.Lamzin, V.S.Wilson, K.S.

(1996) Acta Crystallogr.,Sect.D 52: 327-344

  • DOI: 10.1107/S0907444995007669
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystals of ribonuclease from Streptomyces aureofaciens diffract to atomic resolution at room temperature. Using synchrotron radiation and an imaging-plate scanner, X-ray data have been recorded to 1.20 A resolution from a crystal of native enzyme an ...

    Crystals of ribonuclease from Streptomyces aureofaciens diffract to atomic resolution at room temperature. Using synchrotron radiation and an imaging-plate scanner, X-ray data have been recorded to 1.20 A resolution from a crystal of native enzyme and to 1.15 A from a crystal of a complex with guanosine-2'-monophosphate. Refinement with anisotropic atomic temperature factors resulted in increased accuracy of the structure. The R factors for the two structures are 10.6 and 10.9%. The estimated r.m.s. error in the coordinates is 0.05 A, less than half that obtained in the previous analysis at 1.7 A resolution. For the well ordered part of the main chain the error falls to below 0.02 A as estimated from inversion of the least-squares matrix. The two independent molecules in the asymmetric unit allowed detailed analysis of peptide planarity and some torsion angles. The high accuracy of the analysis revealed density for a partially occupied anion in the nucleotide binding site of molecule A in the native structure which was not seen at lower resolution. The anisotropic model allowed correction of the identity of the residue at position 72 from cysteine to threonine. Cys72 SG had been modelled in previous analyses with two conformations. The solvent structure was modelled by means of an automated procedure employing a set of objective criteria. The solvent structure for models refined using different programs with isotropic and anisotropic description of thermal motion is compared.


    Related Citations: 
    • Complex of Ribonuclease Sa with a Cyclic Nucleotide and a Proposed Model for the Reaction Intermediate
      Sevcik, J.,Zegers, I.,Wyns, L.,Dauter, Z.,Wilson, K.S.
      (1993) Eur.J.Biochem. 216: 301
    • Exocellular Ribonuclease from Streptomyces Aureofaciens. II. Properties and Specificity
      Zelinkova, E.,Bacova, M.,Zelinka, J.
      (1971) Biochim.Biophys.Acta 235: 343
    • 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
    • Determination and Restrained Least-Squares Refinement of the Structures of Ribonuclease Sa and its Complex with 3'-Guanylic Acid at 1.8 A Resolution
      Sevcik, J.,Dodson, E.J.,Dodson, G.G.
      (1991) Acta Crystallogr.,Sect.B 47: 240
    • Amino Acid Sequence Determination of Guanyl-Specific Ribonuclease Sa from Streptomyces Aureofaciens
      Shlyapnikov, S.V.,Both, V.,Kulikov, V.A.,Dementiev, A.A.,Sevcik, J.,Zelinka, J.
      (1986) FEBS Lett. 209: 335
    • Exocellular Ribonuclease from Streptomyces Aureofaciens. I. Isolation and Purification
      Bacova, M.,Zelinkova, E.,Zelinka, J.
      (1971) Biochim.Biophys.Acta 235: 335
    • Complex of Ribonuclease from Streptomyces Aureofaciens with 2'-Gmp at 1.7A Resolution
      Sevcik, J.,Hill, C.P.,Dauter, Z.,Wilson, K.S.
      (1993) Acta Crystallogr.,Sect.D 49: 257


    Organizational Affiliation

    Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE
A, B
96Kitasatospora aureofaciensGene Names: rnaSA
EC: 3.1.27.3
Find proteins for P05798 (Kitasatospora aureofaciens)
Go to UniProtKB:  P05798
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.820α = 90.00
b = 78.560β = 90.00
c = 39.050γ = 90.00
Software Package:
Software NamePurpose
SHELXL-93phasing
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-93model building
SHELXL-93refinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance