PDBsum entry 4blc

Oxidoreductase

PDB id: 4blc

Contents

Protein chains

499 a.a. *

Ligands

HEM ×4

NDP ×4

Waters ×384

* Residue conservation analysis

PDB id:

4blc

Name:

Oxidoreductase

Title:

The structure of orthorhombic crystals of beef liver catalase

Structure:

Protein (catalase). Chain: a, b, c, d. Other_details: each subunit contains a heme and an NADP

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: liver. Other_details: purchased from sigma chemical co., St.Louis, mo

Biol. unit:

Tetramer (from PQS)

Resolution:

2.30Å R-factor: 0.205 R-free: 0.273

Authors:

T.P.Ko,J.Day,A.Malkin,A.Mcpherson

Key ref:

T.P.Ko et al. (1999). Structure of orthorhombic crystals of beef liver catalase. Acta Crystallogr D Biol Crystallogr, 55, 1383-1394. PubMed id: 10417406 DOI: 10.1107/S0907444999007052

Date:

27-Sep-98 Release date: 14-Oct-98

Protein chains

P00432  (CATA_BOVIN) -  Catalase from Bos taurus

Seq: 527 a.a.

Struc: 499 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.11.1.6 - catalase.
• Reaction: 2 H2O2 = O2 + 2 H2O
• Cofactor: Heme; Mn(2+)

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity) Mn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444999007052

Acta Crystallogr D Biol Crystallogr 55:1383-1394 (1999)

PubMed id: 10417406

Structure of orthorhombic crystals of beef liver catalase.

T.P.Ko, J.Day, A.J.Malkin, A.McPherson.

ABSTRACT

The growth mechanisms and physical properties of the orthorhombic crystal form of beef liver catalase were investigated using in situ atomic force microscopy (AFM). It was observed that the crystals grow in the <001> direction by an unusual progression of sequential two-dimensional nuclei of half unit-cell layers corresponding to the 'bottoms' and 'tops' of unit cells. These were easily discriminated by their alternating asymmetric shapes and their strong growth-rate anisotropy. This pattern has not previously been observed with other macromolecular crystals. Orthorhombic beef liver catalase crystals exhibit an extremely high defect density and incorporate great numbers of misoriented microcrystals, revealed intact by etching experiments, which may explain their marginal diffraction properties. To facilitate interpretation of AFM results in terms of intermolecular interactions, the structure of the orthorhombic crystals, having an entire tetramer of the enzyme as the asymmetric unit, was solved by molecular replacement using a model derived from a trigonal crystal form. It was subsequently refined by conventional techniques. Although the packing of molecules in the two unit cells was substantially different, with very few exceptions no significant differences in the molecular structures were observed. In addition, no statistically significant deviation from ideal 222 molecular symmetry appeared within the tetramer. The packing of molecules in the crystal revealed by X-ray analysis explained in a satisfying way the process of crystal growth revealed by AFM.

Selected figure(s)

Figure 4.
Figure 4 A 5 × 5 µm atomic force micrograph of the (001) surface of an orthorhombic beef liver catalase crystal showing step edges and two-dimensional islands. The roughness of the edges suggests the presence and incorporation of high levels of macromolecular impurities which retard normal step advancement at sites of addition.

Figure 9.
Figure 9 A 42 × 42 µm area recorded by AFM on the (001) surface of an orthorhombic catalase crystal which has been slightly etched near equilibrium conditions. This procedure reveals defects and incorporated impurities including incorporated microcrystals which are misoriented with respect to the underlying lattice. Here, it can be seen that there is a striking number of such misoriented microcrystals dispersed throughout the crystal, some as long as 10 µm.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 1383-1394) copyright 1999.

Figures were selected by an automated process.