PDBsum entry 1vkq

Hydrolase

PDB id: 1vkq

Contents

Protein chain

123 a.a. *

Ligands

MPD ×3

Metals

_CA

_CL

Waters ×165

* Residue conservation analysis

PDB id:

1vkq

Name:

Hydrolase

Title:

A re-determination of the structure of the triple mutant (k53,56,120m) of phospholipase a2 at 1.6a resolution using sulphur-sas at 1.54a wavelength

Structure:

Phospholipase a2. Chain: a. Synonym: phosphatidylcholine 2-acylhydrolase, group ib phospholipase a2. Engineered: yes. Mutation: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.179 R-free: 0.217

Authors:

K.Sekar,D.Velmurugan,V.Rajakannan,T.Yamane,M.Dauter,Z.Dauter

Key ref:

K.Sekar et al. (2004). A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6 A resolution using sulfur-SAS at 1.54 A wavelength. Acta Crystallogr D Biol Crystallogr, 60, 1586-1590. PubMed id: 15333929 DOI: 10.1107/S090744490401697X

Date:

12-Jun-04 Release date: 31-Aug-04

Protein chain

P00593  (PA21B_BOVIN) -  Phospholipase A2 from Bos taurus

Seq: 145 a.a.

Struc: 123 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.4 - phospholipase A2.
• Reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3- phosphocholine + a fatty acid + H⁺
• Cofactor: Ca(2+)

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

reference

DOI no: 10.1107/S090744490401697X

Acta Crystallogr D Biol Crystallogr 60:1586-1590 (2004)

PubMed id: 15333929

A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6 A resolution using sulfur-SAS at 1.54 A wavelength.

K.Sekar, V.Rajakannan, D.Velmurugan, T.Yamane, R.Thirumurugan, M.Dauter, Z.Dauter.

ABSTRACT

The crystal structure of the triple mutant K53,56,120M of bovine pancreatic phospholipase A(2) has been redetermined using sulfur single-wavelength anomalous scattering. The synchrotron data were collected at lambda = 1.54 A and the crystal diffracted to 1.6 A resolution. The program SOLVE was used to locate the heavy atoms and to estimate the initial phases and the resulting map was then subjected to RESOLVE. The output of 455 non-H atoms, including 12 S atoms, one calcium ion and one chloride ion, were then subjected to ARP/wARP followed by REFMAC. With the improved phases, the automatic model building successfully built more than 85% of the 123 residues, excluding the N- and C-terminal residues. The final crystallographic R factor is 17.7% (R(free) = 21.7%). The refined model consists of 954 non-H protein atoms, 165 water O atoms, three 2-methyl-2,4-pentanediol (MPD) molecules, one calcium ion and one chloride ion. The present work is yet another example that shows the utility of single-wavelength anomalous scattering data for solving a protein structure.

Selected figure(s)

Figure 2.
Figure 2 A stereoview of the omit electron-density map showing the chloride ion and its liganded atoms. Contours are shown at 1.2 .

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1586-1590) copyright 2004.

Figure was selected by an automated process.