3JW1 | pdb_00003jw1

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

• PDB DOI: https://doi.org/10.2210/pdb3JW1/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2009-09-17 Released: 2009-10-06 
• Deposition Author(s): Larson, S.B., Day, J.S., Nguyen, C., Cudney, R., Mcpherson, A., Center for High-Throughput Structural Biology (CHTSB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.253 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

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 Struct Biol Cryst Commun 66: 113-120

• PubMed: 20124705 
• DOI: https://doi.org/10.1107/S174430910905194X
• Primary Citation Related Structures: 
  3JW1


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.07 kDa 
• Atom Count: 2,203 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	C [auth A], D [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.253 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.73	α = 90
b = 74.85	β = 107.8
c = 50.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Larson, S.B., Day, J.S., Nguyen, C., Cudney, R., Mcpherson, A., Center for High-Throughput Structural Biology (CHTSB)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary