1ROB | pdb_00001rob

STRUCTURE OF THE CRYSTALLINE COMPLEX OF CYTIDYLIC ACID (2'-CMP) WITH RIBONUCLEASE AT 1.6 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1ROB/pdb

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


• Deposited: 1993-08-23 Released: 1994-01-31 
• Deposition Author(s): Lisgarten, J.N., Palmer, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 
  0.237 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Structure of the crystalline complex of cytidylic acid (2'-CMP) with ribonuclease at 1.6 A resolution. Conservation of solvent sites in RNase-A high-resolution structures.

Lisgarten, J.N., Gupta, V., Maes, D., Wyns, L., Zegers, I., Palmer, R.A., Dealwis, C.G., Aguilar, C.F., Hemmings, A.M.

(1993) Acta Crystallogr D Biol Crystallogr 49: 541-547

• PubMed: 15299491 
• DOI: https://doi.org/10.1107/S090744499300719X
• Primary Citation Related Structures: 
  1ROB


• PubMed Abstract: 
  

  The X-ray structure of the inhibitor complex of bovine ribonuclease A with cytidylic acid (2'-CMP) has been determined at 1.6 A resolution and refined by restrained least squares to R = 0.17 for 11 945 reflections. Binding of the inhibitor molecule to the protein is confirmed to be in the productive mode associated with enzyme activity. A study of conserved solvent sites amongst high-resolution structures in the same crystal form reveals a stabilizing water cluster between the N and C termini.

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Organizational Affiliation: 
• Department of Ultrastructure, Institut voor Molekulaire Biologie, Vrije Universiteit Brussel, Sint Genesius Rode, Belgium.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.03 kDa 
• Atom Count: 1,077 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE A	A	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
C2P	B [auth A]	CYTIDINE-2'-MONOPHOSPHATE C9 H14 N3 O8 P YQUAKORMLHPSLZ-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work:  0.237 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.512	α = 90
b = 38.242	β = 106.1
c = 53.303	γ = 90

Software Package:

Software Name	Purpose
RESTRAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Lisgarten, J.N., Palmer, R.A.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Structure summary