9FJ7 | pdb_00009fj7

Nuclease NucB from Bacillus licheniformis mutant N117Q

PDB DOI: https://doi.org/10.2210/pdb9FJ7/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Bacillus licheniformis
Expression System: Bacillus subtilis
Mutation(s): Yes

Deposited: 2024-05-30 Released: 2025-06-11
Deposition Author(s): Koval, T., Stransky, J., Oestergaard, L.H., Dohnalek, J.
Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, Czech Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.163 (Depositor), 0.147 (DCC)
R-Value Work:
0.125 (Depositor), 0.128 (DCC)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of novel nuclease NucB from Bacillus licheniformis

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

To be published.

Macromolecule Content

Total Structure Weight: 12.13 kDa
Atom Count: 1,210
Modeled Residue Count: 110
Deposited Residue Count: 110
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease	A [auth AAA]	110	Bacillus licheniformis	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q65J43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.163 (Depositor), 0.147 (DCC)
R-Value Work: 0.125 (Depositor), 0.128 (DCC)
R-Value Observed: 0.129 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.497	α = 90
b = 53.497	β = 90
c = 84.596	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Oestergaard, L.H.

Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2023042
Czech Academy of Sciences	Czech Republic	RVO 86652036

Revision History (Full details and data files)

Version 1.0: 2025-06-11
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.