6BCH | pdb_00006bch

I-LtrI E29D bound to cognate substrate (nicked complex)

• PDB DOI: https://doi.org/10.2210/pdb6BCH/pdb
• NAKB: 6BCH

• Classification: HYDROLASE/DNA
• Organism(s): Leptographium truncatum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-20 Released: 2018-10-24 
• Deposition Author(s): Brown, C., Zhang, K., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.306 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

I-LtrI E29D bound to cognate substrate (nicked complex)

McMurrough, T.A., Brown, C., Zhang, K., Junop, M., Gloor, G.B., Edgell, D.R.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 208.94 kDa 
• Atom Count: 12,855 
• Modeled Residue Count: 1,368 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein 3/homing endonuclease-like fusion protein	A, E [auth D], I [auth H], M [auth L]	315	Leptographium truncatum	Mutation(s): 1  Gene Names: HEG fusion, rps3
UniProt
Find proteins for C7SWF3 (Leptographium truncatum) Explore C7SWF3  Go to UniProtKB:  C7SWF3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')	B, F [auth E], J [auth I], N	16	Leptographium truncatum

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	C, G [auth F], K [auth J], O	26	Leptographium truncatum

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')	D [auth X], H [auth G], L [auth K], P	11	Leptographium truncatum

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.306 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.76	α = 90.03
b = 66.315	β = 90.03
c = 169.924	γ = 90.22

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Brown, C., Zhang, K., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M.

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references