Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.6 kDa 
• Atom Count: 959 
• Modelled Residue Count: 75 
• Deposited Residue Count: 80 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1JKP

Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations

• PDB DOI:  https://doi.org/10.2210/pdb1JKP/pdb
• NDB: PD0235

• Classification: DNA BINDING PROTEIN/DNA
• Mutation(s): No 


• Deposited: 2001-07-13 Released: 2002-02-22 
• Deposition Author(s): Chiu, T.K., Sohn, C., Johnson, R.C., Dickerson, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.328 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 

Literature

Testing water-mediated DNA recognition by the Hin recombinase.

Chiu, T.K., Sohn, C., Dickerson, R.E., Johnson, R.C.

(2002) EMBO J 21: 801-814

• PubMed: 11847127 
• DOI: https://doi.org/10.1093/emboj/21.4.801
• Primary Citation of Related Structures:  
  1IJW, 1JJ6, 1JJ8, 1JKO, 1JKP, 1JKQ, 1JKR


• PubMed Abstract: 
  

The Hin recombinase specifically recognizes its DNA-binding site by means of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a recombination half-site that were solved as part of the present study, have revealed that two ordered water molecules are present within the major groove interface. In this report, we test the importance of these waters directly by X-ray crystal structure analysis of complexes with four mutant DNA sequences. These structures, combined with their Hin-binding properties, provide strong support for the critical importance of one of the intermediate waters. A lesser but demonstrable role is ascribed to the second water molecule. The mutant structures also illustrate the prominent roles of thymine methyls both in stabilizing intermediate waters and in interfering with water or amino acid side chain interactions with DNA.

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Related Citations: 

• How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase
  Chiu, T.K.
  (2001) Thesis --: 145

• Hin Recombinase Bound to DNA: The Origin of Specificity in Major and Minor Groove Interactions
  Feng, J.A., Johnson, R.C., Dickerson, R.E.
  (1994) Science 263: 348

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-INVERTASE HIN	C	52	N/A	Mutation(s): 0
UniProt
Find proteins for P03013 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P03013  Go to UniProtKB:  P03013

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*GP*AP*AP*GP*A)-3'	A	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*CP*TP*TP*CP*TP*CP*AP*AP*AP*AP*AP*C)-3'	B	14	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1JKP	Kd: 2.05 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.328 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.362	α = 90
b = 81.543	β = 90
c = 45.39	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-22 
Deposition Author(s): Chiu, T.K., Sohn, C., Johnson, R.C., Dickerson, R.E.

Revision History  

• Version 1.0: 2002-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance