1BP7 | pdb_00001bp7

GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA

• PDB DOI: https://doi.org/10.2210/pdb1BP7/pdb
• NAKB: 1BP7

• Classification: TRANSCRIPTION/DNA
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-08-13 Released: 1999-01-06 
• Deposition Author(s): Jurica, M.S., Monnat Junior, R.J., Stoddard, B.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.281 (Depositor) 
• R-Value Work: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI.

Jurica, M.S., Monnat Jr., R.J., Stoddard, B.L.

(1998) Mol Cell 2: 469-476

• PubMed: 9809068 
• DOI: https://doi.org/10.1016/s1097-2765(00)80146-x
• Primary Citation Related Structures: 
  1BP7


• PubMed Abstract: 
  

  The structure of the LAGLIDADG intron-encoded homing endonuclease I-CreI bound to homing site DNA has been determined. The interface is formed by an extended, concave beta sheet from each enzyme monomer that contacts each DNA half-site, resulting in direct side-chain contacts to 18 of the 24 base pairs across the full-length homing site. The structure indicates that I-CreI is optimized to its role in genetic transposition by exhibiting long site-recognition while being able to cleave many closely related target sequences. DNA cleavage is mediated by a compact pair of active sites in the I-CreI homodimer, each of which contains a separate bound divalent cation.

---

Organizational Affiliation: 
• Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington 98109, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.7 kDa 
• Atom Count: 6,915 
• Modeled Residue Count: 704 
• Deposited Residue Count: 704 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (I-CREI)	E [auth A], F [auth B], G [auth C], H [auth D]	152	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii) Explore P05725  Go to UniProtKB:  P05725

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3')	A [auth 1], C [auth 3]	24	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3')	B [auth 2], D [auth 4]	24	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth 1], J [auth 3], K [auth A], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.281 (Depositor) 
• R-Value Work:  0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.556	α = 90
b = 89.259	β = 90
c = 177.516	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-06 
Deposition Author(s): Jurica, M.S., Monnat Junior, R.J., Stoddard, B.L.

Revision History  

• Version 1.0: 1999-01-06
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description