PDBsum entry 1r6j

Membrane protein

PDB id: 1r6j

Contents

Protein chain

82 a.a. *

Metals

_CL

Waters ×237

* Residue conservation analysis

PDB id:

1r6j

Name:

Membrane protein

Title:

Ultrahigh resolution crystal structure of syntenin pdz2

Structure:

Syntenin 1. Chain: a. Fragment: pdz2 domain (residues 197-273). Synonym: syndecan binding protein 1, melanoma differentiation associated protein-9, mda-9, scaffold protein pbp1, pro-tgf-alpha cytoplasmic domain-interacting protein 18, tacip18. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: sdcbp or mda9 or sycl. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

0.73Å R-factor: 0.075 R-free: 0.087

Authors:

B.S.Kang,Y.Devedjiev,U.Derewenda,Z.S.Derewenda

Key ref:

B.S.Kang et al. (2004). The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography. J Mol Biol, 338, 483-493. PubMed id: 15081807 DOI: 10.1016/j.jmb.2004.02.057

Date:

15-Oct-03 Release date: 04-May-04

Protein chain

O00560  (SDCB1_HUMAN) -  Syntenin-1 from Homo sapiens

Seq: 298 a.a.

Struc: 82 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2004.02.057

J Mol Biol 338:483-493 (2004)

PubMed id: 15081807

The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography.

B.S.Kang, Y.Devedjiev, U.Derewenda, Z.S.Derewenda.

ABSTRACT

The crystal structure of the second PDZ domain of the scaffolding protein syntenin was solved using data extending to 0.73 A resolution. The crystallographic model, including the hydrogen atoms and the anisotropic displacement parameters, was refined to a conventional R-factor of 7.5% and Rfree of 8.7%, making it the most precise crystallographic model of a protein molecule to date. The model reveals discrete disorder in several places in the molecule, and significant plasticity of the peptide bond, with some omega angles deviating by nearly 20 degrees from planarity. Most hydrogen atoms are easily identifiable in the electron density and weak hydrogen bonds of the C-H...O type are clearly visible between the beta-strands. The study sets a new standard for high-resolution protein crystallography.

Selected figure(s)

Figure 1.
Figure 1. Electron density maps around the disordered N terminus of synPDZ2. The 2F[o] -F[c] electron density map (blue) and F[o] -F[c] difference electron density map (red) from the structure with major conformer alone are contoured at +4.0 s. Major and minor conformers of residues Met194 to Arg197 are shown as thick and thin frame, respectively. The Figures were generated using O.[20.]

Figure 4.
Figure 4. Examples of electron density maps revealing the position of hydrogen atoms. The 2F[o] -F[c] electron density map (gray) is contoured at +1.0 s, while the F[o] -F[c] difference electron density map (red) prior to inclusion of hydrogen atoms is contoured at +3.0 s and superimposed. A, Ile218; B, Lys203; C, Leu258; and D, Ile247.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 338, 483-493) copyright 2004.

Figures were selected by an automated process.