Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 81.81 kDa 
• Atom Count: 4,759 
• Modelled Residue Count: 513 
• Deposited Residue Count: 662 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3EBC

Structure of N141A HincII with Cognate DNA

• PDB DOI: 10.2210/pdb3EBC/pdb
• NDB: PD1181

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


• Deposited: 2008-08-27 Released: 2008-12-23 
• Deposition Author(s): Little, E.J., Babic, A.C., Horton, N.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.279 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 

Literature

Early Interrogation and Recognition of DNA Sequence by Indirect Readout

Little, E.J., Babic, A.C., Horton, N.C.

(2008) Structure 16: 1828-1837

• PubMed: 19081059 
• DOI: 10.1016/j.str.2008.09.009
• Primary Citation of Related Structures:  
  3EBC


• PubMed Abstract: 
  

Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type-2 restriction enzyme HincII	A, B	317	Haemophilus influenzae	Mutation(s): 1  Gene Names: hincIIR EC: 3.1.21.4
UniProt
Find proteins for P17743 (Haemophilus influenzae) Explore P17743  Go to UniProtKB:  P17743

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DGP*DGP*DGP*DC)-3'	C [auth E]	14	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DC)-3'	D [auth F]	14	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.279 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.551	α = 90
b = 91.571	β = 107.46
c = 70.594	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Little, E.J., Babic, A.C., Horton, N.C.

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations