5USE

5-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate

Fang, Z.Dantsu, Y.Chen, C.Zhang, W.Huang, Z.

(2023) ChemistrySelect 8


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease HC [auth A]142Halalkalibacterium halodurans C-125Mutation(s): 1 
Gene Names: rnhABH0863
EC: 3.1.26.4
UniProt
Find proteins for Q9KEI9 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KEI9 
Go to UniProtKB:  Q9KEI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KEI9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')A [auth B]6synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*GP*(T5S)P*CP*G)-3')B [auth C]6synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.912α = 90
b = 37.56β = 96.17
c = 62.258γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-04
    Changes: Data collection, Refinement description