1A6M

OXY-MYOGLOBIN, ATOMIC RESOLUTION

Summary for 1A6M

• Entry DOI: 10.2210/pdb1a6m/pdb
• Descriptor: MYOGLOBIN, SULFATE ION, PROTOPORPHYRIN IX CONTAINING FE, ... (5 entities in total)
• Functional Keywords: heme protein, model compounds, oxygen storage, ligand binding geometry, conformational substates, oxygen transport
• Biological source: Physeter catodon (sperm whale)
• Total number of polymer chains: 1
• Total formula weight: 17890.38

Authors

Vojtechovsky, J.,Chu, K.,Berendzen, J.,Sweet, R.M.,Schlichting, I. (deposition date: 1998-02-26, release date: 1999-04-06, Last modification date: 2024-05-22)

Primary citation

Vojtechovsky, J.,Chu, K.,Berendzen, J.,Sweet, R.M.,Schlichting, I.
Crystal structures of myoglobin-ligand complexes at near-atomic resolution.
Biophys.J., 77:2153-2174, 1999

PubMed Abstract: We have used x-ray crystallography to determine the structures of sperm whale myoglobin (Mb) in four different ligation states (unligated, ferric aquomet, oxygenated, and carbonmonoxygenated) to a resolution of better than 1.2 A. Data collection and analysis were performed in as much the same way as possible to reduce model bias in differences between structures. The structural differences among the ligation states are much smaller than previously estimated, with differences of <0.25 A root-mean-square deviation among all atoms. One structural parameter previously thought to vary among the ligation states, the proximal histidine (His-93) azimuthal angle, is nearly identical in all the ferrous complexes, although the tilt of the proximal histidine is different in the unligated form. There are significant differences, however, in the heme geometry, in the position of the heme in the pocket, and in the distal histidine (His-64) conformations. In the CO complex the majority conformation of ligand is at an angle of 18 +/- 3 degrees with respect to the heme plane, with a geometry similar to that seen in encumbered model compounds; this angle is significantly smaller than reported previously by crystallographic studies on monoclinic Mb crystals, but still significantly larger than observed by photoselection. The distal histidine in unligated Mb and in the dioxygenated complex is best described as having two conformations. Two similar conformations are observed in MbCO, in addition to another conformation that has been seen previously in low-pH structures where His-64 is doubly protonated. We suggest that these conformations of the distal histidine correspond to the different conformational substates of MbCO and MbO(2) seen in vibrational spectra. Full-matrix refinement provides uncertainty estimates of important structural parameters. Anisotropic refinement yields information about correlated disorder of atoms; we find that the proximal (F) helix and heme move approximately as rigid bodies, but that the distal (E) helix does not.

PubMed: 10512835

Experimental method

X-RAY DIFFRACTION (1 Å)