1KF3

Atomic Resolution Structure of RNase A at pH 5.9

Summary for 1KF3

• Entry DOI: 10.2210/pdb1kf3/pdb
• Related: 1KF2 1KF4 1KF5 1KF7 1KF8
• Descriptor: pancreatic ribonuclease, SULFATE ION (3 entities in total)
• Functional Keywords: rnase a, titration, ph, crystal, soaking, hydrolase
• Biological source: Bos taurus (cattle)
• Cellular location: Secreted: P61823
• Total number of polymer chains: 1
• Total formula weight: 13804.39

Authors

Berisio, R.,Sica, F.,Lamzin, V.S.,Wilson, K.S.,Zagari, A.,Mazzarella, L. (deposition date: 2001-11-19, release date: 2001-12-19, Last modification date: 2024-10-30)

Primary citation

Berisio, R.,Sica, F.,Lamzin, V.S.,Wilson, K.S.,Zagari, A.,Mazzarella, L.
Atomic resolution structures of ribonuclease A at six pH values.
Acta Crystallogr.,Sect.D, 58:441-450, 2002

PubMed Abstract: The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.

PubMed: 11856829
DOI: 10.1107/S0907444901021758

Experimental method

X-RAY DIFFRACTION (1.05 Å)