5LIZ | pdb_00005liz

The structure of Nt.BspD6I nicking endonuclease with all cysteines mutated by serine residues at 0.19 nm resolution .

• PDB DOI: https://doi.org/10.2210/pdb5LIZ/pdb

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


• Deposited: 2016-07-16 Released: 2017-08-02 
• Deposition Author(s): Kachalova, G.S., Artyukh, R.I., Perevyazova, T.A., Yunusova, A.K., Popov, A.N., Bartunik, H.D., Zheleznaya, L.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structural features of Cysteine residues mutation 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: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 71.73 kDa 
• Atom Count: 5,062 
• Modeled Residue Count: 584 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicking endonuclease N.BspD6I	A	610	Bacillus sp. (in: firmicutes)	Mutation(s): 4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.867	α = 90
b = 93.059	β = 112.89
c = 76.58	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Kachalova, G.S., Artyukh, R.I., Perevyazova, T.A., Yunusova, A.K., Popov, A.N., Bartunik, H.D., Zheleznaya, L.A.

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description