3FBD | pdb_00003fbd

Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA

• PDB DOI: https://doi.org/10.2210/pdb3FBD/pdb
• NAKB: 3FBD

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


• Deposited: 2008-11-19 Released: 2009-11-03 
• Deposition Author(s): Wang, Y.T., Doudeva, L.G., Yuan, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Redesign of high-affinity nonspecific nucleases with altered sequence preference

Wang, Y.T., Wright, J.D., Doudeva, L.G., Jhang, H.C., Lim, C., Yuan, H.S.

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)

Macromolecule Content 

• Total Structure Weight: 52.39 kDa 
• Atom Count: 3,663 
• Modeled Residue Count: 335 
• Deposited Residue Count: 336 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E7	A, D	132	Escherichia coli	Mutation(s): 1  Gene Names: cea, colE7 EC: 3.1
UniProt
Find proteins for Q47112 (Escherichia coli) Explore Q47112  Go to UniProtKB:  Q47112

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DAP*DTP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DC)-3'	B, C, E, F	18	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.587	α = 90
b = 49.423	β = 102.64
c = 92.4	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Wang, Y.T., Doudeva, L.G., Yuan, H.S.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description