6G3B | pdb_00006g3b

AvaII restriction endonuclease in complex with an RNA/DNA hybrid

• PDB DOI: https://doi.org/10.2210/pdb6G3B/pdb
• NAKB: 6G3B

• Classification: HYDROLASE
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-24 Released: 2019-04-10 
• Deposition Author(s): Kisiala, M., Kowalska, M., Czapinska, H., Bochtler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

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 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.18 kDa 
• Atom Count: 4,906 
• Modeled Residue Count: 472 
• Deposited Residue Count: 498 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II site-specific deoxyribonuclease	A, B	238	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: alr0933

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*UP*AP*GP*GP*AP*CP*CP*AP*UP*G)-3')	C	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*TP*GP*GP*TP*CP*CP*TP*A)-3')	D	11	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.68	α = 90
b = 104.05	β = 93.27
c = 78.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing
ARP/wARP	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Kisiala, M., Kowalska, M., Czapinska, H., Bochtler, M.

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Funding Organization	Location	Grant Number
	Poland	UMO-2011/02/A/NZ1/00052
	Poland	UMO-2014/13/B/NZ1/03991
	Poland	UMO-2014/14/M/NZ5/00558
	Poland	0295/B/PO1/2008/34
	Poland	N N301 425038
	Poland	N N301 028 934

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2020-05-20
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references