1C54 | pdb_00001c54

SOLUTION STRUCTURE OF RIBONUCLEASE SA

• PDB DOI: https://doi.org/10.2210/pdb1C54/pdb
• BMRB: 4259

• Classification: HYDROLASE
• Organism(s): Kitasatospora aureofaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-10-22 Released: 2001-11-28 
• Deposition Author(s): Laurents, D.V., Canadillas-Perez, J.M., Santoro, J., Schell, D., Pace, C.N., Rico, M., Bruix, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 20 
• Selection Criteria: LOWEST ENERGY AND REPRESENTATIVE OF DIFFERENT CONFORMERS 

Literature

Solution structure and dynamics of ribonuclease Sa.

Laurents, D., Perez-Canadillas, J.M., Santoro, J., Rico, M., Schell, D., Pace, C.N., Bruix, M.

(2001) Proteins 44: 200-211

• PubMed: 11455593 
• DOI: https://doi.org/10.1002/prot.1085
• Primary Citation Related Structures: 
  1C54


• PubMed Abstract: 
  

  We have used NMR methods to characterize the structure and dynamics of ribonuclease Sa in solution. The solution structure of RNase Sa was obtained using the distance constraints provided by 2,276 NOEs and the C6-C96 disulfide bond. The 40 resulting structures are well determined; their mean pairwise RMSD is 0.76 A (backbone) and 1.26 A (heavy atoms). The solution structures are similar to previously determined crystal structures, especially in the secondary structure, but exhibit new features: the loop composed of Pro 45 to Ser 48 adopts distinct conformations and the rings of tyrosines 51, 52, and 55 have reduced flipping rates. Amide protons with greatly reduced exchange rates are found predominantly in interior beta-strands and the alpha-helix, but also in the external 3/10 helix and edge beta-strand linked by the disulfide bond. Analysis of (15)N relaxation experiments (R1, R2, and NOE) at 600 MHz revealed five segments, consisting of residues 1-5, 28-31, 46-50, 60-65, 74-77, retaining flexibility in solution. The change in conformation entropy for RNase SA folding is smaller than previously believed, since the native protein is more flexible in solution than in a crystal.

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Organizational Affiliation: 
• Instituto de Estructura de la Materia, CSIC, Madrid, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.58 kDa 
• Atom Count: 746 
• Modeled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE SA	A	96	Kitasatospora aureofaciens	Mutation(s): 0  EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P05798 (Kitasatospora aureofaciens) Explore P05798  Go to UniProtKB:  P05798

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 20 
• Selection Criteria: LOWEST ENERGY AND REPRESENTATIVE OF DIFFERENT CONFORMERS 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-28 
Deposition Author(s): Laurents, D.V., Canadillas-Perez, J.M., Santoro, J., Schell, D., Pace, C.N., Rico, M., Bruix, M.

Revision History  

• Version 1.0: 2001-11-28
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-10-09
  Changes: Structure summary