4OPJ

Bh-RNaseH:tcdA-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.541 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes.

Egli, M.Pallan, P.S.

(--) Methods Mol.Biol. 1320: 111-126

  • DOI: 10.1007/978-1-4939-2763-0_8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The DNA dodecamer 5'-d(CGCGAATTCGCG)-3' is arguably the best studied oligonucleotide and crystal structures of duplexes with this sequence account for a considerable portion of the total number of oligo-2'-deoxynucleotide structures determined over t ...

    The DNA dodecamer 5'-d(CGCGAATTCGCG)-3' is arguably the best studied oligonucleotide and crystal structures of duplexes with this sequence account for a considerable portion of the total number of oligo-2'-deoxynucleotide structures determined over the last 30 years. The dodecamer has commonly served as a template to analyze the effects of sequence on DNA conformation, the conformational properties of chemically modified nucleotides, DNA-ligand interactions as well as water structure and DNA-cation binding. Although molecular replacement is the phasing method of choice given the large number of available models of the dodecamer, this strategy often fails as a result of conformational changes caused by chemical modification, mismatch pairs, or differing packing modes. Here, we describe an alternative approach to determine crystal structures of the dodecamer in cases where molecular replacement does not produce a solution or when crystals of the DNA alone cannot be grown. It is based on the discovery that many dodecamers of the above sequence can be readily co-crystallized with Bacillus halodurans RNase H, whereby the enzyme is unable to cleave the DNA. Determination of the structure of the complex using the protein portion as the search model yields a structural model of the DNA. Provided crystals of the DNA alone are also available, the DNA model from the complex then enables phasing their structures by molecular replacement.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN, 37232-0146, USA, martin.egli@vanderbilt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H
A, C
142Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Mutation(s): 1 
Gene Names: rnhA
EC: 3.1.26.4
Find proteins for Q9KEI9 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KEI9
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*AP*(TCY)P*TP*TP*CP*GP*CP*G)-3'B,D12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TCY
Query on TCY
B, D
DNA linkingC13 H16 N5 O6 PDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.541 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.162 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.387α = 100.87
b = 47.501β = 101.77
c = 55.216γ = 89.75
Software Package:
Software NamePurpose
MD2data collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-05 
  • Released Date: 2015-02-11 
  • Deposition Author(s): Pallan, P.S., Egli, M.

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references