Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 27.03 kDa 
• Atom Count: 2060 
• Modelled Residue Count: 217 
• Deposited Residue Count: 237 
• Unique protein chains: 1

1GPP

Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I

• PDB DOI: 10.2210/pdb1GPP/pdb

• Classification: ENDONUCLEASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-11-07 Released: 2002-09-19 
• Deposition Author(s): Werner, E., Wende, W., Pingoud, A., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.189 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 

Literature

High Resolution Crystal Structure of Domain I of the Saccharomyces Cerevisiae Homing Endonuclease Pi-Scei

Werner, E., Wende, W., Pingoud, A., Heinemann, U.

(2002) Nucleic Acids Res 30: 3962

• PubMed: 12235380 
• DOI: 10.1093/nar/gkf523
• Primary Citation of Related Structures:  
  1GPP


• PubMed Abstract: 
  

The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the approximately 35 bp recognition sequence. At 1.35 A resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75 degrees bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18.

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Organizational Affiliation: 

Crystallography Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDONUCLEASE PI-SCEI	A	237	Saccharomyces cerevisiae	Mutation(s): 4  EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17255  Go to UniProtKB:  P17255

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.189 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.856	α = 90
b = 47.595	β = 121.41
c = 60.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-07 
• Released Date: 2002-09-19 
Deposition Author(s): Werner, E., Wende, W., Pingoud, A., Heinemann, U.

Revision History  

• Version 1.0: 2002-09-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Advisory, Data collection