3JW1

Crystal Structure of Bovine Pancreatic Ribonuclease Complexed with Uridine-5'-monophosphate at 1.60 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution.

Larson, S.B.Day, J.S.Nguyen, C.Cudney, R.McPherson, A.

(2010) Acta Crystallogr.,Sect.F 66: 113-120

  • DOI: 10.1107/S174430910905194X

  • PubMed Abstract: 
  • Bovine pancreatic ribonuclease A (RNase A) was crystallized from a mixture of small molecules containing basic fuchsin, tobramycin and uridine 5'-monophosphate (U5P). Solution of the crystal structure revealed that the enzyme was selectively bound to ...

    Bovine pancreatic ribonuclease A (RNase A) was crystallized from a mixture of small molecules containing basic fuchsin, tobramycin and uridine 5'-monophosphate (U5P). Solution of the crystal structure revealed that the enzyme was selectively bound to U5P, with the pyrimidine ring of U5P residing in the pyrimidine-binding site at Thr45. The structure was refined to an R factor of 0.197 and an R(free) of 0.253.


    Related Citations: 
    • Progress in the Development of an Alternative Approach to Macromolecular Crystallization
      Larson, S.B.,Day, J.S.,Nguyen, C.,Cudney, R.,Mcpherson, A.
      (2008) CRYST.GROWTH DES. 8: 3038
    • A novel strategy for the crystallization of proteins: X-ray diffraction validation.
      Larson, S.B.,Day, J.S.,Cudney, R.,McPherson, A.
      (2007) Acta Crystallogr.,Sect.D 63: 310
    • Searching for silver bullets: an alternative strategy for crystallizing macromolecules.
      McPherson, A.,Cudney, B.
      (2006) J.Struct.Biol. 156: 387


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
Gene Names: RNASE1 (RNS1)
EC: 3.1.27.5
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 30.730α = 90.00
b = 74.850β = 107.80
c = 50.520γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description