1R6J

Ultrahigh resolution Crystal Structure of syntenin PDZ2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.73 Å
  • R-Value Free: 0.087 
  • R-Value Work: 0.075 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2004) J.Mol.Biol. 338: 483-493

  • DOI: 10.1016/j.jmb.2004.02.057

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Syntenin 1
A
82Homo sapiensMutation(s): 0 
Gene Names: SDCBP (MDA9, SYCL)
Find proteins for O00560 (Homo sapiens)
Go to Gene View: SDCBP
Go to UniProtKB:  O00560
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.73 Å
  • R-Value Free: 0.087 
  • R-Value Work: 0.075 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 25.876α = 90.00
b = 39.544β = 109.64
c = 32.276γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
SCALEPACKdata scaling
HKL-2000data reduction
SHELXmodel building
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance