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PDBsum entry 1cjr

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1cjr
Jmol
Contents
Protein chains
15 a.a.
101 a.a. *
Ligands
SO4
Waters ×54
* Residue conservation analysis
PDB id:
1cjr
Name: Hydrolase
Title: X-ray crystallographic studies of denaturation in ribonuclease s
Structure: Protein (ribonuclease s). Chain: a. Fragment: s peptide. Other_details: synthetic peptide. Protein (ribonuclease s). Chain: b. Fragment: s protein. Synonym: rnase s
Source: Synthetic construct. Organism_taxid: 32630. Other_details: synthetic s peptide. Bos taurus. Cattle. Organism_taxid: 9913. Organelle: pancreas
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.245     R-free:   0.270
Authors: G.S.Ratnaparkhi,R.Varadarajan
Key ref:
G.S.Ratnaparkhi and R.Varadarajan (1999). X-ray crystallographic studies of the denaturation of ribonuclease S. Proteins, 36, 282-294. PubMed id: 10409822 DOI: 10.1002/(SICI)1097-0134(19990815)36:3<282::AID-PROT3>3.3.CO;2-6
Date:
19-Apr-99     Release date:   07-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
15 a.a.
Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
101 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     1 term  

 

 
DOI no: 10.1002/(SICI)1097-0134(19990815)36:3<282::AID-PROT3>3.3.CO;2-6 Proteins 36:282-294 (1999)
PubMed id: 10409822  
 
 
X-ray crystallographic studies of the denaturation of ribonuclease S.
G.S.Ratnaparkhi, R.Varadarajan.
 
  ABSTRACT  
 
In an attempt to view the onset of urea denaturation in ribonuclease we have collected X-ray diffraction data on ribonuclease S crystals soaked in 0, 1.5, 2, 3, and 5 molar urea. At concentrations above 2 M urea, crystals were stabilized by glutaraldehyde crosslinking. We have also collected data on ribonuclease S crystals at low pH in an attempt to study the onset of pH denaturation. The resolution of the datasets range from 1.9 to 3.0 A. Analysis of the structures reveals an increase in disorder with increasing urea concentration. In the 5 M urea structure, this increase in disorder is apparent all over the structure but is larger in loop and helical regions than in the beta strands. The low pH structure shows a very similar pattern of increased disorder. In addition there is a major change in the position of the main chain (> 1 A) in the 65-72 turn region. This region has previously been shown to be involved in one of the initial steps of unfolding in the reduction of ribonuclease A. Crystallographic analyses in the presence of denaturant, when combined with controlled crosslinking, can thus provide detailed structural information that is related to the initial steps of unfolding in solution. Proteins 1999;36:282-294.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Analysis of water in the high resolution structures. A: RMSD plot. B: B-factor plot.
Figure 6.
Figure 6. Ribbon diagram of RNase S coloured according to value of B factor of the main-chain atoms for (A) 5 M and (B) pH 2* structure. Regions of high, intermediate and low B (Å^2) are colored red, white, and blue respectively (scale inset). The figure was generated using the program INSIGHT-II.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (1999, 36, 282-294) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
11742124 E.Chatani, R.Hayashi, H.Moriyama, and T.Ueki (2002).
Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 A resolution.
  Protein Sci, 11, 72-81.
PDB codes: 1eic 1eid 1eie 1fs3
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