5LHC

The structure of D456A mutant of Nt.BspD6I nicking endonuclease at 0.24 nm resolution .

• PDB DOI: https://doi.org/10.2210/pdb5LHC/pdb
• Entry: 5LHC supersedes: 4WL5

• Classification: HYDROLASE
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-07-10 Released: 2017-08-16 
• Deposition Author(s): Kachalova, G.S., Yunusova, A.K., Popov, A.N., Artyukh, R.I., Perevyazova, T.A., Bartunik, H.D., Zheleznaya, L.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.195 
• R-Value Observed: 0.199 

Literature

Structural implication of activity loss by D456A mutant of the nicking endonuclease Nt.BspD6I.

Kachalova, G.S., Yunusova, A.K., Popov, A.N., Artyukh, R.I., Perevyazova, T.A., Bartunik, H.D., Zheleznaya, L.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 144.06 kDa 
• Atom Count: 9,854 
• Modelled Residue Count: 1,161 
• Deposited Residue Count: 1,220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicking endonuclease N.BspD6I	A, B	610	Bacillus sp. (in: firmicutes)	Mutation(s): 1
UniProt
Find proteins for Q8GCA3 (Bacillus sp) Explore Q8GCA3  Go to UniProtKB:  Q8GCA3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth A], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.195 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.35	α = 90
b = 92.666	β = 105.75
c = 113.969	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Kachalova, G.S., Yunusova, A.K., Popov, A.N., Artyukh, R.I., Perevyazova, T.A., Bartunik, H.D., Zheleznaya, L.A.
• This entry supersedes: 4WL5

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description