1KC6

HincII Bound to Cognate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.

Horton, N.C.Dorner, L.F.Perona, J.J.

(2002) Nat.Struct.Mol.Biol. 9: 42-47

  • DOI: 10.1038/nsb741
  • Also Cited By: 1TX3

  • PubMed Abstract: 
  • The crystal structure of the HincII restriction endonuclease-DNA complex shows that degenerate specificity for blunt-ended cleavage at GTPyPuAC sequences arises from indirect readout of conformational preferences at the center pyrimidine-purine step. ...

    The crystal structure of the HincII restriction endonuclease-DNA complex shows that degenerate specificity for blunt-ended cleavage at GTPyPuAC sequences arises from indirect readout of conformational preferences at the center pyrimidine-purine step. Protein-induced distortion of the DNA is accomplished by intercalation of glutamine side chains into the major groove on either side of the recognition site, generating bending by either tilt or roll at three distinct loci. The intercalated side chains propagate a concerted shift of all six target-site base pairs toward the minor groove, producing an unusual cross-strand purine stacking at the center pyrimidine-purine step. Comparison of the HincII and EcoRV cocrystal structures suggests that sequence-dependent differences in base-stacking free energies are a crucial underlying factor mediating protein recognition by indirect readout.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, and Interdepartmental Program in Biomolecular Science and Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-9510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TYPE II RESTRICTION ENZYME HINCII
A, B, C, D
257Haemophilus influenzaeGene Names: hincIIR
EC: 3.1.21.4
Find proteins for P17743 (Haemophilus influenzae)
Go to UniProtKB:  P17743
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'E,F,G,H12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.219 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.120α = 90.00
b = 177.670β = 90.00
c = 256.360γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SOLVEphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-07
    Type: Initial release
  • Version 1.1: 2008-05-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance