6S48

AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report



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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type II site-specific deoxyribonuclease
A, B
238Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: alr0933
Find proteins for Q8YYB7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q8YYB7
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*TP*GP*GP*TP*CP*CP*TP*AP*C)-3')C11synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*AP*G)-3')D, H4synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*CP*CP*AP*TP*C)-3')E, I7synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*TP*G)-3')F4synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*CP*CP*TP*AP*C)-3')G7synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download CCD File 
B
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SER
Query on SER

Download CCD File 
B
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
BME
Query on BME

Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.129α = 90
b = 116.21β = 102.91
c = 56.774γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing
ARP/wARPmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release