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
  • Structures With Same Primary Citation

  • 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 1A82Homo sapiensMutation(s): 0 
Gene Names: SDCBP OR MDA9 OR SYCLSDCBPMDA9SYCL
Find proteins for O00560 (Homo sapiens)
Explore O00560 
Go to UniProtKB:  O00560
NIH Common Fund Data Resources
PHAROS  O00560
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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
b = 39.544β = 109.64
c = 32.276γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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