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- PDB-6ejt: Nuclease NucB from Bacillus licheniformis in P21 space group -

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Basic information

Entry
Database: PDB / ID: 6ejt
TitleNuclease NucB from Bacillus licheniformis in P21 space group
ComponentsNuclease
KeywordsHYDROLASE / nuclease / DNAse / metal dependent
Function / homologyNuclease
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Jan 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 1.2Oct 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)24,86711
Polymers24,0032
Non-polymers8659
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The enzyme forms dimers in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-129 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.228, 47.821, 100.234
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, soaked in 0.02 M 3'-AMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98148 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013
RadiationMonochromator: 2 MIRRORS AND A DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98148 Å / Relative weight: 1
ReflectionResolution: 1.7→47.82 Å / Num. obs: 22140 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 14.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.026 / Rrim(I) all: 0.037 / Net I/σ(I): 21.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 8.3 / Num. unique obs: 963 / CC1/2: 0.99 / Rpim(I) all: 0.078 / Rrim(I) all: 0.114 / % possible all: 75.2

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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: 6EJS

6ejs


Resolution: 1.7→47.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.112
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1089 4.9 %RANDOM
Rwork0.196 ---
obs0.197 22121 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.46 Å2 / Biso mean: 20.2163 Å2 / Biso min: 6.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.58 Å2
2---0.74 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 45 287 2008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191845
X-RAY DIFFRACTIONr_bond_other_d00.021653
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.972508
X-RAY DIFFRACTIONr_angle_other_deg3.74833835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48121.95487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57515306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1461523
X-RAY DIFFRACTIONr_chiral_restr0.1010.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022100
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02419
X-RAY DIFFRACTIONr_mcbond_it1.6041.748908
X-RAY DIFFRACTIONr_mcbond_other1.5971.746907
X-RAY DIFFRACTIONr_mcangle_it2.4282.6111143
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 78 -
Rwork0.219 1319 -
all-1397 -
obs--77.87 %

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