PDBsum entry 2a7c

Hydrolase

PDB id: 2a7c

Contents

Protein chain

240 a.a. *

Ligands

SO4 ×2

GOL

Metals

_XE

Waters ×222

* Residue conservation analysis

PDB id:

2a7c

Name:

Hydrolase

Title:

On the routine use of soft x-rays in macromolecular crystallography, part iii- the optimal data collection wavelength

Structure:

Elastase 1. Chain: a. Ec: 3.4.21.36

Source:

Sus scrofa. Pig. Organism_taxid: 9823

Resolution:

1.65Å R-factor: 0.156 R-free: 0.182

Authors:

C.Mueller-Dieckmann,S.Panjikar,P.A.Tucker,M.S.Weiss

Key ref:

C.Mueller-Dieckmann et al. (2005). On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength. Acta Crystallogr D Biol Crystallogr, 61, 1263-1272. PubMed id: 16131760 DOI: 10.1107/S0907444905021475

Date:

05-Jul-05 Release date: 19-Jul-05

Protein chain

P00772  (CELA1_PIG) -  Chymotrypsin-like elastase family member 1 from Sus scrofa

Seq: 266 a.a.

Struc: 240 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.36 - pancreatic elastase.
• Reaction: Hydrolysis of proteins, including elastin. Preferential cleavage: Ala-|-Xaa.

DOI no: 10.1107/S0907444905021475

Acta Crystallogr D Biol Crystallogr 61:1263-1272 (2005)

PubMed id: 16131760

On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.

C.Mueller-Dieckmann, S.Panjikar, P.A.Tucker, M.S.Weiss.

ABSTRACT

Complete and highly redundant data sets were collected at different wavelengths between 0.80 and 2.65 A for a total of ten different protein and DNA model systems. The magnitude of the anomalous signal-to-noise ratio as assessed by the quotient R(anom)/R(r.i.m.) was found to be influenced by the data-collection wavelength and the nature of the anomalously scattering substructure. By utilizing simple empirical correlations, for instance between the estimated deltaF/F and the expected R(anom) or the data-collection wavelength and the expected R(r.i.m.), the wavelength at which the highest anomalous signal-to-noise ratio can be expected could be estimated even before the experiment. Almost independent of the nature of the anomalously scattering substructure and provided that no elemental X-ray absorption edge is nearby, this optimal wavelength is 2.1 A.

Selected figure(s)

Figure 1.
Figure 1 Estimated anomalous diffraction ratio [Delta] F/F in the wavelength range 0.5-3.0 Å for the ten model systems described in this paper. The estimate is for zero scattering angle and assumes resolved and independent anomalous scatterers. The ten systems are separated into two groups (Xe group and P/S/Ca group) and sorted in decreasing strength of the anomalous signal. Black lines, ConA-Xe, adaptin-Xe, PPE-Xe and HEL-Xe; blue line, thermolysin; green lines, DNA, HEL, trypsin, thaumatin and PPE-Ca. The experimentally determined anomalously scattering substructures for the ten systems were (1) ConA-Xe: two protein S atoms, one Mn2+ and one Ca^2+ ion, both fully occupied, as well as six Xe atoms with occupancies (q) of 0.40, 0.30, 0.20, 0.15, 0.15 and 0.10; (2) adaptin-Xe: four protein S atoms and two Xe atoms (q = 0.32 and 0.10); (3) PPE-Xe: ten protein S atoms, one Xe atom (q = 0.72) and two SO[4]^2- ions (q = 0.70 and 0.50); (4) HEL-Xe: ten S atoms, two Xe atoms (q = 0.24 and 0.08), the first one being situated on a crystallographic twofold axis, and eight Cl- ions (q = 0.68, 0.58, 0.52, 0.37, 0.37, 0.34, 0.31 and 0.28); (5) DNA: eight P atoms; (6) HEL: ten S atoms and seven Cl- ions (q = 0.80, 0.77, 0.70, 0.60, 0.57, 0.37 and 0.25); (7) thermolysin: two protein S atoms, six Ca^2+ ions (q = 1.00, 1.00, 1.00, 1.00, 0.50 and 0.25), one fully occupied Zn2+ ion and two DMSO molecules (q = 0.50 and 0.40); (8) trypsin: 14 protein S atoms, one fully occupied Ca^2+ ion and two partially occupied Cl- ions (q = 0.40 and 0.25); (9) thaumatin: 17 protein S atoms and (10) PPE-Ca: ten protein S atoms, one Ca^2+ ion (q = 0.81) and one Cl- ion (q = 0.30).

Figure 4.
Figure 4 Dependence of the observed R*[r.i.m] values on the data-collection wavelength. The data distribution can be fitted with the exponential function R*[r.i.m] = 3.78 + 0.0002exp(3.76 [lambda] ) and an R2 value of 0.57. The three outliers (DNA data sets collected at [lambda] = 2.10, 2.30 and 2.50 Å, respectively) not obeying the exponential fit are shown as open circles.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1263-1272) copyright 2005.

Figures were selected by an automated process.