PDBsum entry 1v96

Structural genomics, unknown function

PDB id: 1v96

Contents

Protein chains

146 a.a. *

Ligands

GOL ×3

Waters ×365

* Residue conservation analysis

PDB id:

1v96

Name:

Structural genomics, unknown function

Title:

Crystal structure of hypothetical protein of unknown function from pyrococcus horikoshii ot3

Structure:

Hypothetical protein ph0500. Chain: a, b. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.75Å R-factor: 0.209 R-free: 0.228

Authors:

J.Jeyakanthan,T.H.Tahirov,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

J.Jeyakanthan et al. (2005). Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii. Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 463-468. PubMed id: 16511069 DOI: 10.1107/S1744309105012406

Date:

21-Jan-04 Release date: 01-Feb-05

Protein chains

O58236  (VAPC4_PYRHO) -  Ribonuclease VapC4 from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 149 a.a.

Struc: 146 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.-.-

DOI no: 10.1107/S1744309105012406

Acta Crystallogr Sect F Struct Biol Cryst Commun 61:463-468 (2005)

PubMed id: 16511069

Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.

J.Jeyakanthan, E.Inagaki, C.Kuroishi, T.H.Tahirov.

ABSTRACT

The Pyrococcus horikoshii OT3 protein PH0500 is highly conserved within the Pyrococcus genus of hyperthermophilic archaea and shows low amino-acid sequence similarity with a family of PIN-domain proteins. The protein has been expressed, purified and crystallized in two crystal forms: PH0500-I and PH0500-II. The structure was determined at 2.0 A by the multiple anomalous dispersion method using a selenomethionyl derivative of crystal form PH0500-I (PH0500-I-Se). The structure of PH0500-I has been refined at 1.75 A resolution to an R factor of 20.9% and the structure of PH0500-II has been refined at 2.0 A resolution to an R factor of 23.4%. In both crystal forms as well as in solution the molecule appears to be a dimer. Searches of the databases for protein-fold similarities confirmed that the PH0500 protein is a PIN-domain protein with possible exonuclease activity and involvement in DNA or RNA editing.

Selected figure(s)

Figure 3.
The overall view of (a) PH0500 and (b) AF0591 dimers and (c) PAE2754 tetramers. Subunits are represented by ribbons and have different colours. The figures were prepared using MOLSCRIPT (Kraulis, 1991[triangle]) and RASTER3D (Merritt & Murphy, 1994[triangle]). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 May 1; 61(Pt 5): 463–468. Published online 2005 April 26. doi: 10.1107/S1744309105012406. Copyright [copyright] International Union of Crystallography 2005

Figure 4.
The surface representation of the PH0500 dimer. View (a) is as in Fig. 3 [triangle] Figure 3-(a) and the view (b) is in the opposite direction to (a). The positively and the negatively charged surface regions are in blue and red, respectively. The figures were prepared using GRASP (Nichols et al., 1991[triangle]). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 May 1; 61(Pt 5): 463–468. Published online 2005 April 26. doi: 10.1107/S1744309105012406. Copyright [copyright] International Union of Crystallography 2005

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2005, 61, 463-468) copyright 2005.

Figures were selected by an automated process.