Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


X-ray structure of a ribonuclease A-uridine vanadate complex at 1.3 A resolution.

Ladner, J.E.Wladkowski, B.D.Svensson, L.A.Sjolin, L.Gilliland, G.L.

(1997) Acta Crystallogr D Biol Crystallogr 53: 290-301

  • DOI: 10.1107/S090744499601582X
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The X-ray crystal structure of a uridine vanadate-ribonuclease A complex has been determined at 1.3 A resolution. The resulting structure includes all 124 amino-acid residues, a uridine vanadate, 131 water molecules, and a single bound 2-methyl-2-pro ...

    The X-ray crystal structure of a uridine vanadate-ribonuclease A complex has been determined at 1.3 A resolution. The resulting structure includes all 124 amino-acid residues, a uridine vanadate, 131 water molecules, and a single bound 2-methyl-2-propanol. Side chains of 11 surface residues showing discrete disorder were modeled with multiple conformations. The final crystallographic R factor is 0.197. Structures obtained from high-level ab initio quantum calculations of model anionic oxyvanadate compounds were used to probe the effects of starting structure on the refinement process and final structure of the penta-coordinate phosphorane analog, uridine vanadate. The least-squares refinement procedure gave rise to the same final structure of the inhibitor despite significantly different starting models. Comparison with the previously determined complex of ribonuclease A with uridine vanadate obtained from a joint X-ray/neutron analysis (6RSA) [Wlodawer, Miller & Sjölin (1983). Proc. Natl Acad. Sci. USA, 80, 3628-3631] reveals similarities in the overall enzyme structure and the relative position of the key active-site residues, Hisl2, His119 and Lys41, but significant differences in the V-O bond distances and angles. The influence of ligand binding on the enzyme structure is assessed by a comparison of the current X-ray structure with the phosphate-free ribonuclease A structure (7RSA) [Wlodawer, Svensson, Sjölin & Gilliland (1988). Biochemistry, 27, 2705-2717]. Ligand binding alters the solvent structure, distribution and number of residues with multiple conformations, and temperature factors of the protein atoms. In fact, the temperature factors of atoms of several residues that interact with the ligand are reduced, but those of the atoms of several residues remote from the active site exhibit marked increases.

    Related Citations: 
    • The Active Site of Bovin Pancreatic Ribonuclease: An Example of Solvent Modulation Specificity
      Gilliland, G.L., Dill, J., Pechik, I., Svensson, L.A., Sjolin, L.
      (1994) Protein Pept Lett 1: 60
    • Structure of Phosphate-Free Ribonuclease A Refined at 1.26 A
      Wlodawer, A., Svensson, L.A., Sjolin, L., Gilliland, G.L.
      (1988) Biochemistry 27: 2705
    • Nuclear Magnetic Resonance and Neutron Diffraction Studies of the Complex of Ribonuclease A with Uridine Vanadate, a Transition-State Analogue
      Borah, B., Chen, C.W., Egan, W., Miller, M., Wlodawer, A., Cohen, J.S.
      (1985) Biochemistry 24: 2058
    • Active Site of Rnase: Neutron Diffraction Study of a Complex with Uridine Vanadate, a Transition-State Analog
      Wlodawer, A., Miller, M., Sjolin, L.
      (1983) Proc Natl Acad Sci U S A 80: 3628

    Organizational Affiliation

    The Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute and National Institute of Standards and Technology, Rockville, MD 20850, USA.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: (PDB Primary Data), (UniProt)
Find proteins for P61823 (Bos taurus)
Go to UniProtKB:  P61823
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on UVC

Download CCD File 
C9 H12 N2 O9 V
 Ligand Interaction
Query on TBU

Download CCD File 
C4 H10 O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.8α = 90
b = 38.2β = 106.1
c = 53.2γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
XENGENdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance