6EJV | pdb_00006ejv

Nuclease NucB from Bacillus licheniformis in sulphate free conditions

• PDB DOI: https://doi.org/10.2210/pdb6EJV/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2017-09-23 Released: 2019-04-10 
• Deposition Author(s): Stransky, J., Dohnalek, J., Oestergaard, L.A.
• Funding Organization(s): European Regional Development Fund, Ministry of Education (Czech Republic)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.167 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structure of novel nuclease NucB from Bacillus licheniformis

Stransky, J., Dohnalek, J., Oestergaard, L.H.

To be published.

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)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 24.12 kDa 
• Atom Count: 2,043 
• Modeled Residue Count: 218 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease	A, B	110	Bacillus licheniformis	Mutation(s): 0  Gene Names: nucB, BL00126
UniProt
Find proteins for Q65J43 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65J43  Go to UniProtKB:  Q65J43

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.167 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.44	α = 90
b = 58.47	β = 90
c = 72.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Stransky, J., Dohnalek, J., Oestergaard, L.A.

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Funding Organization	Location	Grant Number
European Regional Development Fund	Czech Republic	CZ.1.05.11.00/02.0109
Ministry of Education (Czech Republic)	Czech Republic	LM2015043
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/16_013/0001776

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary