1dy5
From Proteopedia
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|PDB= 1dy5 |SIZE=350|CAPTION= <scene name='initialview01'>1dy5</scene>, resolution 0.87Å | |PDB= 1dy5 |SIZE=350|CAPTION= <scene name='initialview01'>1dy5</scene>, resolution 0.87Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IAS:BETA-ASPARTYL+RESIDUE+(GAMMA-LINKED)'>IAS</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dy5 OCA], [http://www.ebi.ac.uk/pdbsum/1dy5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dy5 RCSB]</span> | ||
}} | }} | ||
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[[Category: Vitagliano, L.]] | [[Category: Vitagliano, L.]] | ||
[[Category: Zagari, A.]] | [[Category: Zagari, A.]] | ||
| - | [[Category: ACT]] | ||
| - | [[Category: IPA]] | ||
| - | [[Category: SO4]] | ||
[[Category: deamidation]] | [[Category: deamidation]] | ||
[[Category: ribonuclease]] | [[Category: ribonuclease]] | ||
[[Category: ultra-high resolution]] | [[Category: ultra-high resolution]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:51:08 2008'' |
Revision as of 16:51, 30 March 2008
| |||||||
| , resolution 0.87Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Pancreatic ribonuclease, with EC number 3.1.27.5 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DEAMIDATED DERIVATIVE OF BOVINE PANCREATIC RIBONUCLEASE
Overview
Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.101 for all observed reflections in the resolution range 61.0-0.87 A. The ratio observations/parameters is 7.2 for the final model. This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. In the present structure it was possible to obtain a more accurate picture of the active site whose electron density was not clearly interpretable in the previous 1.9 A resolution structure. In particular, the P1 site is alternatively occupied either by a sulphate anion or by a water molecule network. Most of hydrogen atoms were visible in the electron density maps, including those involved in C(alpha)-H(alpha).O interactions. Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. This correlation can be fruitfully used as a valuable tool in protein structure validation.
About this Structure
1DY5 is a Single protein structure of sequence from Bos taurus. Full crystallographic information is available from OCA.
Reference
The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis., Esposito L, Vitagliano L, Sica F, Sorrentino G, Zagari A, Mazzarella L, J Mol Biol. 2000 Mar 31;297(3):713-32. PMID:10731423
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