5J9A

Ambient temperature transition state structure of arginine kinase - crystal 11/Form II

Summary for 5J9A

• Entry DOI: 10.2210/pdb5j9a/pdb
• Related: 5J99
• Descriptor: Arginine kinase, NITRATE ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: arginine kinase ambient temperature, transferase
• Biological source: Limulus polyphemus (Atlantic horseshoe crab)
• Total number of polymer chains: 1
• Total formula weight: 40938.48

Authors

Godsey, M.,Davulcu, O.,Nix, J.,Skalicky, J.J.,Bruschweiler, R.,Chapman, M.S. (deposition date: 2016-04-08, release date: 2016-08-17, Last modification date: 2023-09-27)

Primary citation

Godsey, M.H.,Davulcu, O.,Nix, J.C.,Skalicky, J.J.,Bruschweiler, R.P.,Chapman, M.S.
The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase.
Structure, 24:1658-1667, 2016

PubMed Abstract: Arginine kinase provides a model for functional dynamics, studied through crystallography, enzymology, and nuclear magnetic resonance. Structures are now solved, at ambient temperature, for the transition state analog (TSA) complex. Analysis of quasi-rigid sub-domain displacements show that differences between the two TSA structures average about 5% of changes between substrate-free and TSA forms, and they are nearly co-linear. Small backbone hinge rotations map to sites that also flex on substrate binding. Anisotropic atomic displacement parameters (ADPs) are refined using rigid-body TLS constraints. Consistency between crystal forms shows that they reflect intrinsic molecular properties more than crystal lattice effects. In many regions, the favored directions of thermal/static displacement are appreciably correlated with movements on substrate binding. Correlation between ADPs and larger substrate-associated movements implies that the latter approximately follow paths of low-energy intrinsic motions.

PubMed: 27594681
DOI: 10.1016/j.str.2016.07.013

Experimental method

X-RAY DIFFRACTION (1.997 Å)