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PDBsum entry 8rat

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Hydrolase (nucleic acid,RNA) PDB id
8rat
Jmol
Contents
Protein chain
124 a.a. *
* Residue conservation analysis
PDB id:
8rat
Name: Hydrolase (nucleic acid,RNA)
Title: Effects of temperature on protein structure and dynamics: x- ray crystallographic studies of the protein ribonuclease-a at nine different temperatures from 98 to 320 k
Structure: Ribonuclease a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.50Å     R-factor:   0.158    
Authors: R.F.Tiltonjunior,J.C.Dewan,G.A.Petsko
Key ref:
R.F.Tilton et al. (1992). Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry, 31, 2469-2481. PubMed id: 1547232 DOI: 10.1021/bi00124a006
Date:
13-Aug-91     Release date:   15-Jul-93    
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  

 

 
DOI no: 10.1021/bi00124a006 Biochemistry 31:2469-2481 (1992)
PubMed id: 1547232  
 
 
Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K.
R.F.Tilton, J.C.Dewan, G.A.Petsko.
 
  ABSTRACT  
 
Structures using X-ray diffraction data collected to 1.5-A resolution have been determined for the protein ribonuclease-A at nine different temperatures ranging from 98 to 320 K. It is determined that the protein molecule expands slightly (0.4% per 100 K) with increasing temperature and that this expansion is linear. The expansion is due primarily to subtle repacking of the molecule, with exposed and mobile loop regions exhibiting the largest movements. Individual atomic Debye-Waller factors exhibit predominantly biphasic behavior, with a small positive slope at low temperatures and a larger positive slope at higher temperatures. The break in this curve occurs at a characteristic temperature of 180-200 K, perhaps indicative of fundamental changes in the dynamical structure of the surrounding protein solvent. The distribution of protein Debye-Waller factors is observed to broaden as well as shift to higher values as the temperature is increased.
 

Literature references that cite this PDB file's key reference

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PDB code: 3jw1
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PDB codes: 3k0m 3k0n 3k0o 3k0p 3k0q
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PDB code: 2oxp
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PDB codes: 2igc 2ntg 2nth 2ou8 2ou9
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PDB codes: 2i16 2i17
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PDB codes: 1yv4 1yv6 1yv7
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PDB codes: 1uxs 1uxw
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Translational hydration water dynamics drives the protein glass transition.
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Many residues in cytochrome c populate alternative states under equilibrium conditions.
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Volumetric properties of proteins.
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Flexibility and packing in proteins.
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11746706 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2002).
Reversible substrate-induced domain motions in ribonuclease A.
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PDB codes: 1jvt 1jvu 1jvv
11856829 R.Berisio, F.Sica, V.S.Lamzin, K.S.Wilson, A.Zagari, and L.Mazzarella (2002).
Atomic resolution structures of ribonuclease A at six pH values.
  Acta Crystallogr D Biol Crystallogr, 58, 441-450.
PDB codes: 1kf2 1kf3 1kf4 1kf5 1kf7 1kf8
12198298 Y.Joti, M.Nakasako, A.Kidera, and N.Go (2002).
Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors.
  Acta Crystallogr D Biol Crystallogr, 58, 1421-1432.
PDB codes: 1iwt 1iwu 1iwv 1iww 1iwx 1iwy 1iwz
11340055 A.G.Palmer (2001).
Nmr probes of molecular dynamics: overview and comparison with other techniques.
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The inverse relationship between protein dynamics and thermal stability.
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Optimization of solvation models for predicting the structure of surface loops in proteins.
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Some thermodynamic implications for the thermostability of proteins.
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11343287 M.Nara, A.Sakamoto, J.Yamamichi, and M.Tasumi (2001).
Temperature dependence of near-IR excited Raman spectra of crystalline hen egg-white lysozyme.
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11264586 M.Weik, G.Kryger, A.M.Schreurs, B.Bouma, I.Silman, J.L.Sussman, P.Gros, and J.Kroon (2001).
Solvent behaviour in flash-cooled protein crystals at cryogenic temperatures.
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11296284 X.W.Fang, B.L.Golden, K.Littrell, V.Shelton, P.Thiyagarajan, T.Pan, and T.R.Sosnick (2001).
The thermodynamic origin of the stability of a thermophilic ribozyme.
  Proc Natl Acad Sci U S A, 98, 4355-4360.  
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Effect of a concentrated "inert" macromolecular cosolute on the stability of a globular protein with respect to denaturation by heat and by chaotropes: a statistical-thermodynamic model.
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10644947 J.W.Mack, M.G.Usha, J.Long, R.G.Griffin, and R.J.Wittebort (2000).
Backbone motions in a crystalline protein from field-dependent 2H-NMR relaxation and line-shape analysis.
  Biopolymers, 53, 9.  
11256577 M.C.Peitsch, T.Schwede, and N.Guex (2000).
Automated protein modelling--the proteome in 3D.
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11106628 M.Tarek, and D.J.Tobias (2000).
The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments.
  Biophys J, 79, 3244-3257.  
10861939 S.D'Auria, P.Herman, J.R.Lakowicz, F.Tanfani, E.Bertoli, G.Manco, and M.Rossi (2000).
The esterase from the thermophilic eubacterium Bacillus acidocaldarius: structural-functional relationship and comparison with the esterase from the hyperthermophilic archaeon Archaeoglobus fulgidus.
  Proteins, 40, 473-481.  
10531512 E.Garman (1999).
Cool data: quantity AND quality.
  Acta Crystallogr D Biol Crystallogr, 55, 1641-1653.  
  10493577 I.V.Kurinov, D.E.Myers, J.D.Irvin, and F.M.Uckun (1999).
X-ray crystallographic analysis of the structural basis for the interactions of pokeweed antiviral protein with its active site inhibitor and ribosomal RNA substrate analogs.
  Protein Sci, 8, 1765-1772.
PDB codes: 1qcg 1qci 1qcj
10512837 R.M.Daniel, J.L.Finney, V.Réat, R.Dunn, M.Ferrand, and J.C.Smith (1999).
Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution.
  Biophys J, 77, 2184-2190.  
  10211838 R.Palma, and P.M.Curmi (1999).
Computational studies on mutant protein stability: The correlation between surface thermal expansion and protein stability.
  Protein Sci, 8, 913-920.  
9449362 B.Yu, and D.L.Caspar (1998).
Structure of cubic insulin crystals in glucose solutions.
  Biophys J, 74, 616-622.  
  9568898 M.Gregoriou, M.E.Noble, K.A.Watson, E.F.Garman, T.M.Krulle, C.de la Fuente, G.W.Fleet, N.G.Oikonomakos, and L.N.Johnson (1998).
The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding.
  Protein Sci, 7, 915-927.
PDB codes: 1a8i 2gpn
  9260285 J.Dunbar, H.P.Yennawar, S.Banerjee, J.Luo, and G.K.Farber (1997).
The effect of denaturants on protein structure.
  Protein Sci, 6, 1727-1733.
PDB codes: 1ddr 1dds 1rbw 1rbx
9348663 J.N.Onuchic, Z.Luthey-Schulten, and P.G.Wolynes (1997).
Theory of protein folding: the energy landscape perspective.
  Annu Rev Phys Chem, 48, 545-600.  
9504803 N.Guex, and M.C.Peitsch (1997).
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
  Electrophoresis, 18, 2714-2723.
PDB code: 2ak6
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Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution.
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PDB codes: 1tal 2ull
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Crystal structure of human interleukin-10 at 1.6 A resolution and a model of a complex with its soluble receptor.
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PDB code: 2ilk
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Intermediate trapping and laue X-ray diffraction: potential for enzyme mechanism, dynamics, and inhibitor screening.
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A perspective on biological catalysis.
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8574702 K.Moffat, and R.Henderson (1995).
Freeze trapping of reaction intermediates.
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Ultrastructure of skeletal muscle fibers studied by a plunge quick freezing method: myofilament lengths.
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Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis.
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Frozen stiff.
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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.