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PDBsum entry 3rn3

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Hydrolase (nucleic acid,RNA) PDB id
3rn3
Jmol
Contents
Protein chain
124 a.a. *
Ligands
SO4
Waters ×107
* Residue conservation analysis
PDB id:
3rn3
Name: Hydrolase (nucleic acid,RNA)
Title: Segmented anisotropic refinement of bovine ribonuclease a by the application of the rigid-body tls model
Structure: Ribonuclease a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.45Å     R-factor:   0.223    
Authors: B.Howlin,D.S.Moss,G.W.Harris,R.A.Palmer
Key ref: B.Howlin et al. (1989). Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model. Acta Crystallogr A, 45, 851-861. PubMed id: 2619965
Date:
30-Oct-91     Release date:   31-Oct-91    
Supersedes: 1rn3
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     6 terms  

 

 
Acta Crystallogr A 45:851-861 (1989)
PubMed id: 2619965  
 
 
Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model.
B.Howlin, D.S.Moss, G.W.Harris.
 
  ABSTRACT  
 
The anisotropic displacements of selected rigid groups in bovine ribonuclease A have been refined from X-ray diffraction data by the application of the rigid-body TLS model. The rigid groups chosen were the side chains of tyrosine, histidine and phenylalanine and the planar side chains of aspartic acid, glutamic acid, glutamine, asparagine and arginine. The method has also been applied to the co-crystallizing active-site sulfate anion. This has enabled the description of the motion of the above-mentioned side-chain atoms by anisotropic displacement ellipsoids from a 1.45 A refinement. The hydrophobic side groups in the protein core show mainly translational motion, with mean-square librations of 20 deg2 which are similar to those found in some close-packed crystals of small organic molecules. Librational displacements are much more significant in the hydrophilic side groups where their magnitudes can be correlated with solvent accessibility. Large librations of some solvent exposed side chains correspond with the breakdown of a simple TLS model and the existence of multiple orientations of the side groups. The TLS model has also been applied to the whole protein molecule and shows that the average motion is approximately isotropic with little librational character.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19289466 P.A.Meyer, P.Ye, M.H.Suh, M.Zhang, and J.Fu (2009).
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data.
  J Biol Chem, 284, 12933-12939.
PDB code: 3fki
19836331 P.B.Moore (2009).
On the relationship between diffraction patterns and motions in macromolecular crystals.
  Structure, 17, 1307-1315.  
19274657 R.Peters (2009).
Translocation through the nuclear pore: Kaps pave the way.
  Bioessays, 31, 466-477.  
18001769 J.E.Lee, E.Bae, C.A.Bingman, G.N.Phillips, and R.T.Raines (2008).
Structural basis for catalysis by onconase.
  J Mol Biol, 375, 165-177.
PDB codes: 2gmk 2i5s
17965184 B.Zhao, R.Lehr, A.M.Smallwood, T.F.Ho, K.Maley, T.Randall, M.S.Head, K.K.Koretke, and C.G.Schnackenberg (2007).
Crystal structure of the kinase domain of serum and glucocorticoid-regulated kinase 1 in complex with AMP PNP.
  Protein Sci, 16, 2761-2769.
PDB code: 2r5t
16301790 D.E.Holloway, G.B.Chavali, M.C.Hares, V.Subramanian, and K.R.Acharya (2005).
Structure of murine angiogenin: features of the substrate- and cell-binding regions and prospects for inhibitor-binding studies.
  Acta Crystallogr D Biol Crystallogr, 61, 1568-1578.
PDB codes: 2bwk 2bwl
16045769 G.N.Hatzopoulos, D.D.Leonidas, R.Kardakaris, J.Kobe, and N.G.Oikonomakos (2005).
The binding of IMP to ribonuclease A.
  FEBS J, 272, 3988-4001.
PDB codes: 1z6d 1z6s
16231289 H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.
  Proteins, 61, 704-721.  
15681654 L.Meinhold, and J.C.Smith (2005).
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease.
  Biophys J, 88, 2554-2563.  
15376253 B.Kuhn, P.A.Kollman, and M.Stahl (2004).
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.
  J Comput Chem, 25, 1865-1872.  
14587072 A.Y.Woody, and R.W.Woody (2003).
Individual tyrosine side-chain contributions to circular dichroism of ribonuclease.
  Biopolymers, 72, 500-513.  
14573867 D.D.Leonidas, G.B.Chavali, N.G.Oikonomakos, E.D.Chrysina, M.N.Kosmopoulou, M.Vlassi, C.Frankling, and K.R.Acharya (2003).
High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors.
  Protein Sci, 12, 2559-2574.
PDB codes: 1o0f 1o0h 1o0m 1o0n 1o0o
12324397 R.E.Georgescu, E.G.Alexov, and M.R.Gunner (2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
  Biophys J, 83, 1731-1748.  
11340657 J.E.Nielsen, and G.Vriend (2001).
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.
  Proteins, 43, 403-412.  
10620274 E.Banachowicz, J.GapiƄski, and A.Patkowski (2000).
Solution structure of biopolymers: a new method of constructing a bead model.
  Biophys J, 78, 70-78.  
10866974 K.Yamamoto, Y.Mizutani, and T.Kitagawa (2000).
Nanosecond temperature jump and time-resolved Raman study of thermal unfolding of ribonuclease A.
  Biophys J, 79, 485-495.  
10091597 E.H.Vatzaki, S.C.Allen, D.D.Leonidas, K.Trautwein-Fritz, J.Stackhouse, S.A.Benner, and K.R.Acharya (1999).
Crystal structure of a hybrid between ribonuclease A and bovine seminal ribonuclease--the basic surface, at 2.0 A resolution.
  Eur J Biochem, 260, 176-182.
PDB code: 1b6v
10388736 E.L.Mehler, and F.Guarnieri (1999).
A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins.
  Biophys J, 77, 3.  
  9521116 A.T.Alexandrescu, K.Rathgeb-Szabo, K.Rumpel, W.Jahnke, T.Schulthess, and R.A.Kammerer (1998).
15N backbone dynamics of the S-peptide from ribonuclease A in its free and S-protein bound forms: toward a site-specific analysis of entropy changes upon folding.
  Protein Sci, 7, 389-402.  
9311977 A.C.Papageorgiou, R.Shapiro, and K.R.Acharya (1997).
Molecular recognition of human angiogenin by placental ribonuclease inhibitor--an X-ray crystallographic study at 2.0 A resolution.
  EMBO J, 16, 5162-5177.
PDB code: 1a4y
9057494 G.Kurapkat, P.Krüger, A.Wollmer, J.Fleischhauer, B.Kramer, E.Zobel, A.Koslowski, H.Botterweck, and R.W.Woody (1997).
Calculations of the CD spectrum of bovine pancreatic ribonuclease.
  Biopolymers, 41, 267-287.  
9370435 X.Raquet, V.Lounnas, J.Lamotte-Brasseur, J.M.Frère, and R.C.Wade (1997).
pKa calculations for class A beta-lactamases: methodological and mechanistic implications.
  Biophys J, 73, 2416-2426.  
8534804 J.Antosiewicz (1995).
Computation of the dipole moments of proteins.
  Biophys J, 69, 1344-1354.  
7964923 B.J.Howlin, N.P.Tomkinson, J.Chen, and G.A.Webb (1994).
Design of potential angiogenin inhibitors.
  J Comput Aided Mol Des, 8, 223-230.  
2011586 J.Kuriyan, and W.I.Weis (1991).
Rigid protein motion as a model for crystallographic temperature factors.
  Proc Natl Acad Sci U S A, 88, 2773-2777.  
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.