1R6J | pdb_00001r6j

Ultrahigh resolution Crystal Structure of syntenin PDZ2

• PDB DOI: https://doi.org/10.2210/pdb1R6J/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-10-15 Released: 2004-05-04 
• Deposition Author(s): Kang, B.S., Devedjiev, Y., Derewenda, U., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.73 Å
• R-Value Free: 
  0.087 (Depositor), 0.080 (DCC) 
• R-Value Work: 
  0.075 (Depositor), 0.078 (DCC) 

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 Biology 338: 483-493

• PubMed: 15081807 
• DOI: https://doi.org/10.1016/j.jmb.2004.02.057
• Primary Citation Related Structures: 
  1R6J


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.75 kDa 
• Atom Count: 964 
• Modeled Residue Count: 82 
• Deposited Residue Count: 82 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin 1	A	82	Homo sapiens	Mutation(s): 0  Gene Names: SDCBP OR MDA9 OR SYCL
UniProt & NIH Common Fund Data Resources
Find proteins for O00560 (Homo sapiens) Explore O00560  Go to UniProtKB:  O00560
PHAROS:  O00560 GTEx:  ENSG00000137575

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.73 Å
• R-Value Free:  0.087 (Depositor), 0.080 (DCC) 
• R-Value Work:  0.075 (Depositor), 0.078 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.876	α = 90
b = 39.544	β = 109.64
c = 32.276	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-04 
Deposition Author(s): Kang, B.S., Devedjiev, Y., Derewenda, U., Derewenda, Z.S.

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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations