3EUY

Crystal Structure of Ribonuclease A in 50% Dioxane

Summary for 3EUY

• Entry DOI: 10.2210/pdb3euy/pdb
• Related: 3EUX 3EUZ 3EV0 3EV1 3EV2 3EV3 3EV4 3EV5 3EV6
• Descriptor: Ribonuclease pancreatic, 1,4-DIETHYLENE DIOXIDE (3 entities in total)
• Functional Keywords: rnase, organic solvents, multiple solvent crystal structures, endonuclease, glycation, glycoprotein, hydrolase, nuclease, secreted
• Biological source: Bos taurus (bovine)
• Cellular location: Secreted: P61823
• Total number of polymer chains: 2
• Total formula weight: 27857.18

Authors

Dechene, M.,Wink, G.,Smith, M.,Swartz, P.,Mattos, C. (deposition date: 2008-10-12, release date: 2009-06-23, Last modification date: 2024-10-30)

Primary citation

Dechene, M.,Wink, G.,Smith, M.,Swartz, P.,Mattos, C.
Multiple solvent crystal structures of ribonuclease A: An assessment of the method
Proteins, 76:861-881, 2009

PubMed Abstract: The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.

PubMed: 19291738
DOI: 10.1002/prot.22393

Experimental method

X-RAY DIFFRACTION (1.95 Å)