3E3T

Structure of porcine pancreatic elastase with the magic triangle I3C

PDB DOI: https://doi.org/10.2210/pdb3E3T/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
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: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.157
R-Value Observed: 0.157

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: 28.51 kDa
Atom Count: 2,235
Modelled Residue Count: 240
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elastase-1	A	240	Sus scrofa	Mutation(s): 0 EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772 Go to UniProtKB: P00772
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00772
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I3C Query on I3C Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid C₈ H₄ I₃ N O₄ JEZJSNULLBSYHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.157
R-Value Observed: 0.157
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.096	α = 90
b = 57.973	β = 90
c = 74.395	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction
SADABS	data scaling
SHELXD	phasing
SHELXL-97	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-28

Deposition Author(s):

Beck, T.

Gruene, T.

Sheldrick, G.M.

Revision History (Full details and data files)

Version 1.0: 2008-10-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-11
Changes: Database references
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary