3GT4

Structure of proteinase K with the magic triangle I3C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The magic triangle goes MAD: experimental phasing with a bromine derivative

Beck, T.Gruene, T.Sheldrick, G.M.

(2010) Acta Crystallogr.,Sect.D 66: 374-380

  • DOI: 10.1107/S0907444909051609
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional gro ...

    Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br K edge was successfully carried out. Radiation damage to the bromine-carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.


    Related Citations: 
    • A magic triangle for experimental phasing of macromolecules
      Beck, T.,Krasauskas, A.,Gruene, T.,Sheldrick, G.M.
      (2008) Acta Crystallogr.,Sect.D 64: 1179


    Organizational Affiliation

    Department of Structural Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany. tbeck@shelx.uni-ac.gwdg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
proteinase K
A
279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Parengyodontium album)
Go to UniProtKB:  P06873
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
I3C
Query on I3C

Download SDF File 
Download CCD File 
A
5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
5-Amino-2,4,6-triiodoisophthalic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.140 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.784α = 90.00
b = 67.784β = 90.00
c = 101.845γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SADABSdata scaling
PDB_EXTRACTdata extraction
SHELXDphasing
SHELXL-97refinement
SHELXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-04-29
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Refinement description