PDBsum entry 1bvc

Oxygen storage

PDB id: 1bvc

Contents

Protein chain

153 a.a. *

Ligands

PO4 ×4

BLA

Waters ×306

* Residue conservation analysis

PDB id:

1bvc

Name:

Oxygen storage

Title:

Structure of a biliverdin apomyoglobin complex (form d) at 118 k

Structure:

Apomyoglobin. Chain: a. Other_details: crystal form d

Source:

Physeter catodon. Sperm whale. Organism_taxid: 9755

Resolution:

1.50Å R-factor: 0.194

Authors:

U.G.Wagner,N.Mueller,W.Schmitzberger,H.Falk,C.Kratky

Key ref:

U.G.Wagner et al. (1995). Structure determination of the biliverdin apomyoglobin complex: crystal structure analysis of two crystal forms at 1.4 and 1.5 A resolution. J Mol Biol, 247, 326-337. PubMed id: 7707378 DOI: 10.1006/jmbi.1994.0142

Date:

16-Dec-94 Release date: 31-Jul-95

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.11.1.- - ?????
• Enzyme class 3: E.C.1.7.-.-

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1006/jmbi.1994.0142

J Mol Biol 247:326-337 (1995)

PubMed id: 7707378

Structure determination of the biliverdin apomyoglobin complex: crystal structure analysis of two crystal forms at 1.4 and 1.5 A resolution.

U.G.Wagner, N.Müller, W.Schmitzberger, H.Falk, C.Kratky.

ABSTRACT

Crystal structure determinations of two orthorhombic (P2(1)2(1)2(1)) crystal modifications of the biliverdin apomyoglobin complex are described. The two structures were determined by X-ray diffraction at 100 K to a resolution of 1.5 A and 1.4 A. Both crystal forms were grown by hanging-drop techniques, using phosphate as precipitant. The structures were solved by molecular replacement and refined to final R-values of 19.4% and 21.2%. Both structures are very similar with respect to the binding site and the conformation of the biliverdin chromophore, which occurs in a (P) helical conformation. It is located within the heme pocket, very close in position and orientation to the heme binding site in myoglobin. Two water molecules not present in the crystal structure of myoglobin are sequestered within the heme pocket in the biliverdin-apomyoglobin complex, and they are engaged in hydrogen bonding to the biliverdin and to the protein. Comparison with structural results from an earlier NMR study of the same complex shows good agreement.

Selected figure(s)

Figure 4.
Figure 4. Schematic representations of the hydrogen bonds involving the biliverdin molecule, the 2 water molecules (WAT2 and WAT1) and the 2 histidine residues (His93 and His64). The interatomic distances given in the Figure are from the crystal structure of blv-Mb-D. The corresponding distances from the crystal structure of blv-Mb-B are as follows: N(His64). . .WAT1, 2.88; WAT1. . .O(A), 2.66; N(B). . .N(His93), 2.95; O(B). . .WAT2, 2.79; WAT2. . .N(His93), 3.29 Å .

Figure 8.
Figure 8. Two disordered residues in the blv-Mb-D crystal structure. The spacial proximity of the 2 residues creates a pair of mutually exclusive conformations in such a way, that the conformation represented by full lines for the one residue is incompatible with the conformation represented by dotted lines for the other residue, and vice versa.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 247, 326-337) copyright 1995.

Figures were selected by an automated process.