PDB-9fj7: Nuclease NucB from Bacillus licheniformis mutant N117Q

ID or keywords:

Entry

Database: PDB / ID: 9fj7

Title

Nuclease NucB from Bacillus licheniformis mutant N117Q

Components

Nuclease

Keywords

DNA BINDING PROTEIN / DNAse / endonuclease / mutant N117Q

Function / homology

Deoxyribonuclease NucA/NucB / Nuclease

Function and homology information

Biological species

Bacillus licheniformis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.25 Å

Authors

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

Funding support

Czech Republic, 2items

Citation

Journal: To Be Published
Title: Structure of novel nuclease NucB from Bacillus licheniformis
Authors: Stransky, J. / Koval, T. / Oestergaard, L.H. / Dohnalek, J.

History

Deposition	May 30, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9fj7.cif.gz	70.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9fj7.ent.gz		Display	PDB format
PDBx/mmJSON format	9fj7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fj7_validation.pdf.gz	430.6 KB	Display	wwPDB validaton report
Full document	9fj7_full_validation.pdf.gz	431.3 KB	Display
Data in XML	9fj7_validation.xml.gz	10.7 KB	Display
Data in CIF	9fj7_validation.cif.gz	15 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fj/9fj7 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/9fj7	HTTPS FTP

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Related structure data

Related structure data	6ejsC 6ejtC 6ejuC 6ejvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Nuclease

hetero molecules

12.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	53.497, 53.497, 84.596
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	AAA-423- HOH

#1: Protein	Nuclease Mass: 12015.358 Da / Num. of mol.: 1 / Mutation: N117Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: nucB, BL00126 / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q65J43
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.9 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: protein concentration was 18 mg/ml; storage buffer: 20mM Tris pH 8.0, 100mM NaCl; reservoir solution: 0.1 M 1,6-Hexanediol 0.1 M 1-Butanol 0.1 M 1,2-Propanediol 0.1 M 2-Propanol 0.1 M 1,4- ...Details: protein concentration was 18 mg/ml; storage buffer: 20mM Tris pH 8.0, 100mM NaCl; reservoir solution: 0.1 M 1,6-Hexanediol 0.1 M 1-Butanol 0.1 M 1,2-Propanediol 0.1 M 2-Propanol 0.1 M 1,4-Butanediol 0.1 M 1,3-Propanediol 0.85 M Tris and Bicine pH 8.5 10.5 % v/v 2-Methyl- -2,4,-pentanediol 10.5 % PEG 1000 10.5 % w/v PEG 3350

Crystal

Density Matthews: 2.92 Å³/Da / Density % sol: 57.9 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein concentration was 18 mg/ml; storage buffer: 20mM Tris pH 8.0, 100mM NaCl; reservoir solution: 0.1 M 1,6-Hexanediol 0.1 M 1-Butanol 0.1 M 1,2-Propanediol 0.1 M 2-Propanol 0.1 M 1,4- ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.25→46.33 Å / Num. obs: 39455 / % possible obs: 100 % / Redundancy: 9.5 % / B_iso Wilson estimate: 12 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.023 / R_rim(I) all: 0.071 / Net I/σ(I): 22.4
Reflection shell	Resolution: 1.25→1.27 Å / Redundancy: 9.7 % / R_merge(I) obs: 1.659 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1926 / CC_1/2: 0.659 / R_pim(I) all: 0.556 / R_rim(I) all: 1.752 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	20210323	data reduction
XSCALE	20210323	data scaling
MOLREP	11.7.03	phasing
Coot	0.8.9.1	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.25→46.33 Å / Cor.coef. F_o:F_c: 0.977 / SU B: 1.132 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.033
Details: Hydrogens have been added in their riding positions. The last reciprocal space refinement was performed against all measured reflections.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16305	2002	5.1 %	Random
R_work	0.12549	39411	-	-
all	0.129	-	-	-
obs	0.12909	39411	99.894 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 17.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.032 Å²	0.016 Å²	0 Å²
2-	-	0.032 Å²	-0 Å²
3-	-	-	-0.105 Å²

Refinement step

Cycle: LAST / Resolution: 1.25→46.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	844	0	8	222	1074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	1028
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.014	963
X-RAY DIFFRACTION	r_angle_refined_deg	1.825	1.655	1414
X-RAY DIFFRACTION	r_angle_other_deg	1.671	1.6	2242
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.072	5	149
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.161	19.846	65
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.015	15	181
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.674	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	133
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	1230
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	264
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	195
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	794
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	435
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	476
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	133
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.163	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.172	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.792	1.411	497
X-RAY DIFFRACTION	r_mcbond_other	1.698	1.406	496
X-RAY DIFFRACTION	r_mcangle_it	2.217	2.123	631
X-RAY DIFFRACTION	r_mcangle_other	2.218	2.125	632
X-RAY DIFFRACTION	r_scbond_it	2.542	1.728	531
X-RAY DIFFRACTION	r_scbond_other	2.54	1.727	532
X-RAY DIFFRACTION	r_scangle_it	3.057	2.472	764
X-RAY DIFFRACTION	r_scangle_other	3.055	2.471	765
X-RAY DIFFRACTION	r_lrange_it	3.734	18.798	1230
X-RAY DIFFRACTION	r_lrange_other	3.331	17.071	1168
X-RAY DIFFRACTION	r_rigid_bond_restr	4.414	3	1991

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	% reflection R_free (%)	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.25-1.282	0.283	136	4.7	0.235	2729	99.6869
1.282-1.318	0.205	126	4.5	0.201	2677	99.8931
1.318-1.356	0.2	137	5.1	0.182	2561	100
1.356-1.397	0.216	155	5.8	0.169	2528	99.9255
1.397-1.443	0.194	143	5.6	0.149	2429	100
1.443-1.494	0.15	122	4.9	0.12	2374	99.9199
1.494-1.55	0.155	136	5.7	0.113	2244	100
1.55-1.613	0.138	99	4.3	0.096	2208	99.8701
1.613-1.685	0.144	110	4.9	0.087	2134	100
1.685-1.767	0.127	126	5.9	0.086	2010	100
1.767-1.863	0.135	113	5.6	0.09	1919	100
1.863-1.975	0.132	93	4.8	0.099	1838	100
1.975-2.111	0.132	74	4.1	0.102	1741	100
2.111-2.28	0.136	90	5.3	0.097	1610	100
2.28-2.497	0.138	82	5.2	0.106	1484	99.8088
2.497-2.791	0.146	64	4.4	0.107	1388	99.9312
2.791-3.221	0.145	74	5.9	0.119	1175	99.6013
3.221-3.94	0.166	74	6.7	0.137	1037	99.9086
3.94-5.552	0.218	37	4.3	0.142	827	99.7691
5.552-46.33	0.285	29	5.5	0.237	495	99.8095

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