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PDBsum entry 3a1r

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protein ligands links
Hydrolase PDB id
3a1r
Jmol
Contents
Protein chain
124 a.a. *
Ligands
DOD ×92
* Residue conservation analysis
PDB id:
3a1r
Name: Hydrolase
Title: Neutron crystal structure analysis of bovine pancreatic ribo
Structure: Ribonuclease pancreatic. Chain: a. Synonym: rnase 1, rnase a. Ec: 3.1.27.5
Source: Bos taurus. Bovine. Organism_taxid: 9913. Other_details: pancreas
Authors: D.Yagi,I.Tanaka,N.Niimura
Key ref: D.Yagi et al. (2009). A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution. Acta Crystallogr D Biol Crystallogr, 65, 892-899. PubMed id: 19690366
Date:
21-Apr-09     Release date:   01-Sep-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: 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!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
Acta Crystallogr D Biol Crystallogr 65:892-899 (2009)
PubMed id: 19690366  
 
 
A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution.
D.Yagi, T.Yamada, K.Kurihara, Y.Ohnishi, M.Yamashita, T.Tamada, I.Tanaka, R.Kuroki, N.Niimura.
 
  ABSTRACT  
 
A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7 A resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high-resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A. Numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines were also determined at 1.7 A resolution. The protonation and deprotonation states of all of the charged amino-acid residues allowed us to provide a definitive description of the hydrogen-bonding network around the active site and the H atoms of the key His48 residue. Differences in hydrogen-bond strengths for the alpha-helices and beta-sheets were inferred from determination of the hydrogen-bond lengths and the H/D-exchange ratios of the backbone amide H atoms. The correlation between the B factors and hydrogen-bond lengths of the hydration water molecules was also determined.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20383004 M.M.Blum, S.J.Tomanicek, H.John, B.L.Hanson, H.Rüterjans, B.P.Schoenborn, P.Langan, and J.C.Chen (2010).
X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 379-385.
PDB code: 3kgg
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.