PDBsum entry 1wc7

Antibody

PDB id: 1wc7

Contents

Protein chains

213 a.a. *

224 a.a. *

Ligands

PP3

Metals

IOD ×5

Waters ×119

* Residue conservation analysis

PDB id:

1wc7

Name:

Antibody

Title:

Fab fragment of plp-dependent catalytic antibody 15a9 in complex with phosphopyridoxyl-l-alanine

Structure:

Fab fragment of catalytic antibody 15a9, light chain. Chain: a, l. Engineered: yes. Fab fragment of catalytic antibody 15a9, heavy chain. Chain: b, h. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: mus musculus. Expression_system_taxid: 10090. Expression_system_cell_line: 15a9 murine hybridoma. Expression_system_cell_line: 15a9 murine hybridoma

Biol. unit:

Dimer (from PDB file)

Resolution:

2.33Å R-factor: 0.223 R-free: 0.309

Authors:

B.Golinelli-Pimpaneau,P.Christen

Key ref:

B.Golinelli-Pimpaneau (2005). Structure of a pseudomerohedrally twinned monoclinic crystal form of a pyridoxal phosphate-dependent catalytic antibody. Acta Crystallogr D Biol Crystallogr, 61, 472-476. PubMed id: 15805602 DOI: 10.1107/S0907444905003331

Date:

09-Nov-04 Release date: 30-Nov-05

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

No UniProt id for this chain

Struc: 224 a.a.

DOI no: 10.1107/S0907444905003331

Acta Crystallogr D Biol Crystallogr 61:472-476 (2005)

PubMed id: 15805602

Structure of a pseudomerohedrally twinned monoclinic crystal form of a pyridoxal phosphate-dependent catalytic antibody.

B.Golinelli-Pimpaneau.

ABSTRACT

The purification, crystallization and structure determination at 2.3 A resolution of the complex of the pyridoxal-5'-phosphate (PLP) dependent catalytic antibody 15A9 with a phosphopyridoxyl-L-alanine (PPL-L-alanine) substrate analogue are described. The crystal belongs to space group P2(1), with two molecules in the asymmetric unit related by non-crystallographic symmetry. The unit-cell parameters are a = 63.5, b = 81.7, c = 79.3 A and beta is fortuitously 90 degrees . Refinement of the structure converged at unacceptably high R factors. Although the traditional analysis of intensity distribution did not indicate twinning, pseudomerohedral twinning was revealed by a newer test based on local intensity differences [Padilla & Yeates (2003), Acta Cryst. D59, 1124-1130]. When the potential twinning operator was included in SHELX, the structure could be satisfactorily refined with a twinning fraction of 0.46, indicating a nearly perfect hemihedrally twinned crystal. One of the active sites is occupied by the phosphopyridoxyl-L-alanine ligand, while one iodide ion mimics the cofactor phosphate group in the other. Four other iodide ions are present in the structure: two are involved in specific intermolecular contacts and two dictate the conformation of the CDRH3 loop in each molecule.

Selected figure(s)

Figure 3.
Figure 3 The iodide ions in the Fab15A9-PPL-L-Ala structure. A [sigma] [A]-weighted F[obs] - F[calc] electron-density map omitting the iodide ions is contoured at the level of 2 [sigma] and superimposed on the active-site structures. (a) Stereoview of the non-occupied active site of the Fab15A9-PPL-L-Ala complex. One iodide ion takes the place of the phosphate group in one molecule of the asymmetric unit. (b) The conformation of CDRH3 is stabilized by an iodide ion. In each molecule of the asymmetric unit, one iodide ion makes four 3.0-3.8 Å interactions with the NH groups of His97 and His99, TrpH100e N [epsilon] 1 and AsnH100a N [delta] 2. (c) One iodide ion interacts with the two molecules of the asymmetric unit. At the corresponding position in the other molecule, one iodide ion is involved in a crystallographic contact.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 472-476) copyright 2005.

Figure was selected by an automated process.