1RBN

THE STRUCTURE OF RIBONUCLEASE A DERIVATIVE II AT 2.1 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of ribonuclease A derivative II at 2.1-A resolution.

Boque, L.Gracia Coll, M.Vilanova, M.Cuchillo, C.M.Fita, I.

(1994) J.Biol.Chem. 269: 19707-19712


  • PubMed Abstract: 
  • The crystal structure of bovine pancreatic ribonuclease A derivative II, a covalent derivative obtained by reaction of 6-chloropurine 9-beta-D-ribofuranosyl 5'-monophosphate with the alpha-amino group of Lys-1, has been determined and refined at 2.1- ...

    The crystal structure of bovine pancreatic ribonuclease A derivative II, a covalent derivative obtained by reaction of 6-chloropurine 9-beta-D-ribofuranosyl 5'-monophosphate with the alpha-amino group of Lys-1, has been determined and refined at 2.1-A resolution with an agreement factor R = 0.166 for 6254 reflections in the resolution shell 8.0 to 2.1 A. Crystals are orthorhombic and belong to space group C222(1) with unit cell parameters a = 75.73 A, b = 57.85 A, and c = 53.26 A. This crystal packing had never been reported before for pancreatic ribonuclease nor its complexes. The structure found is in accordance with the location of p2, B3, and R3 subsites at the N-terminal region of the protein and provides an explanation of the catalytic behavior observed for this derivative. In particular, differences in kinetic parameters and in the pKa value of His-119 between derivative II and native ribonuclease A can be interpreted on the basis of the position of the phosphate moiety within the derivative structure. Some uncertainty remains on the nucleotide sugar conformation determined.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P5P
Query on P5P

Download SDF File 
Download CCD File 
A
PURINE RIBOSIDE-5'-MONOPHOSPHATE
C10 H13 N4 O7 P
MCWDCZIDTUQRHK-FDDDBJFASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.730α = 90.00
b = 57.850β = 90.00
c = 53.260γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-03-29 
  • Released Date: 1994-12-20 
  • Deposition Author(s): Boque, L., Fita, I.

Revision History 

  • Version 1.0: 1994-12-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance