1RUV

RIBONUCLEASE A-URIDINE VANADATE COMPLEX: HIGH RESOLUTION RESOLUTION X-RAY STRUCTURE (1.3 A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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

Literature

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.,Sect.D 53: 290-301

  • DOI: 10.1107/S090744499601582X

  • 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: 
    • 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
    • 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.USA 80: 3628
    • 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
    • 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


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE A
A
124Bos taurusMutation(s): 0 
Gene Names: RNASE1 (RNS1)
EC: 4.6.1.18
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TBU
Query on TBU

Download SDF File 
Download CCD File 
A
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
UVC
Query on UVC

Download SDF File 
Download CCD File 
A
URIDINE-2',3'-VANADATE
C9 H12 N2 O9 V
JSPAHXDHRUTBDP-ODQFIEKDSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 29.800α = 90.00
b = 38.200β = 106.10
c = 53.200γ = 90.00
Software Package:
Software NamePurpose
XENGENdata collection
PROFFTrefinement
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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