6G3B

AvaII restriction endonuclease in complex with an RNA/DNA hybrid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation

Kisiala, M., Kowalska, M., Pastor, M., Korza, H., Czapinska, H., Bochtler, M.

(2020) Nucleic Acids Res 


Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type II site-specific deoxyribonuclease
A, B
238Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: alr0933
UniProt
Find proteins for Q8YYB7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YYB7 
Go to UniProtKB:  Q8YYB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YYB7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*UP*AP*GP*GP*AP*CP*CP*AP*UP*G)-3')11synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*AP*TP*GP*GP*TP*CP*CP*TP*A)-3')11synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.68α = 90
b = 104.05β = 93.27
c = 78.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
ARP/wARPmodel building

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
PolandUMO-2011/02/A/NZ1/00052
PolandUMO-2014/13/B/NZ1/03991
PolandUMO-2014/14/M/NZ5/00558
Poland0295/B/PO1/2008/34
PolandN N301 425038
PolandN N301 028 934

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references