3E3S

Structure of thaumatin with the magic triangle I3C

PDB DOI: https://doi.org/10.2210/pdb3E3S/pdb

Classification: PLANT PROTEIN
Organism(s): Thaumatococcus daniellii
Mutation(s): No

Deposited: 2008-08-08 Released: 2008-10-28
Deposition Author(s): Beck, T., Gruene, T., Sheldrick, G.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.210
R-Value Work: 0.158
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A magic triangle for experimental phasing of macromolecules

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

(2008) Acta Crystallogr D Biol Crystallogr 64: 1179-1182

PubMed: 19020357 Search on PubMed
DOI: https://doi.org/10.1107/S0907444908030266
Primary Citation of Related Structures:
3E3D, 3E3S, 3E3T

PubMed Abstract:
Obtaining phase information for the solution of macromolecular structures is still one of the bottlenecks in X-ray crystallography. 5-Amino-2,4,6-triiodoisophthalic acid (I3C), in which three covalently bound iodines form an equilateral triangle, was incorporated into proteins in order to obtain phases by single-wavelength anomalous dispersion (SAD). An improved binding capability compared with simple heavy-metal ions, ready availability, improved recognition of potential heavy-atom sites and low toxicity make I3C particularly suitable for experimental phasing.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 25.33 kDa
Atom Count: 1,888
Modelled Residue Count: 207
Deposited Residue Count: 207
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin I	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883 Go to UniProtKB: P02883
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I3C Query on I3C Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid C₈ H₄ I₃ N O₄ JEZJSNULLBSYHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]