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- PDB-6eju: Nuclease NucB from Bacillus licheniformis in P1 space group -

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Basic information

Entry
Database: PDB / ID: 6eju
TitleNuclease NucB from Bacillus licheniformis in P1 space group
ComponentsNuclease
KeywordsHYDROLASE / nuclease / DNAse / metal dependent
Function / homologyDeoxyribonuclease NucA/NucB / Nuclease
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStransky, J. / Dohnalek, J. / Oestergaard, L.A.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
Ministry of Education (Czech Republic)LM2015043 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
CitationJournal: To Be Published
Title: Structure of novel nuclease NucB from Bacillus licheniformis
Authors: Stransky, J. / Dohnalek, J. / Oestergaard, L.H.
History
DepositionSep 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclease
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,77110
Polymers24,0032
Non-polymers7698
Water4,360242
1
A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4826
Polymers12,0011
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2904
Polymers12,0011
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.227, 48.000, 52.203
Angle α, β, γ (deg.)75.510, 89.530, 89.600
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nuclease


Mass: 12001.333 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: putative EC 3.1.21.1 / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: nucB, BL00126 / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q65J43
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8 M ammonium sulfate, 0.1 M sodium acetate pH 4.6 0.02 M MnCl2 (soaked)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.823 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013
RadiationMonochromator: 2 MIRROR AND DOUBLE-CRYSTAL MONCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.823 Å / Relative weight: 1
ReflectionResolution: 1.9→46.47 Å / Num. obs: 15502 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.43 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.034 / Rrim(I) all: 0.056 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 722 / CC1/2: 0.639 / Rpim(I) all: 0.148 / Rrim(I) all: 0.236 / % possible all: 64.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ejt

6ejt


Resolution: 1.9→46.47 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 795 5.1 %RANDOM
Rwork0.1736 ---
obs0.1738 15489 90.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.54 Å2 / Biso mean: 25.4376 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.34 Å2-1.05 Å2
2---0.12 Å20.77 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 40 242 1958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191766
X-RAY DIFFRACTIONr_bond_other_d00.021566
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9652387
X-RAY DIFFRACTIONr_angle_other_deg3.73333627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20822.38184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36615285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.271520
X-RAY DIFFRACTIONr_chiral_restr0.090.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021987
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02393
X-RAY DIFFRACTIONr_mcbond_it1.8922.254876
X-RAY DIFFRACTIONr_mcbond_other1.8552.25875
X-RAY DIFFRACTIONr_mcangle_it2.7863.3691093
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 38 -
Rwork0.333 809 -
all-847 -
obs--67.01 %

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