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- PDB-6ejs: Nuclease NucB from Bacillus licheniformis in P212121 space group -

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Basic information

Entry
Database: PDB / ID: 6ejs
TitleNuclease NucB from Bacillus licheniformis in P212121 space group
ComponentsNuclease
KeywordsHYDROLASE / nuclease / DNAse / metal dependent
Function / homologyDeoxyribonuclease NucA/NucB / Deoxyribonuclease NucA/NucB / Nuclease
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2904
Polymers12,0011
Non-polymers2883
Water2,504139
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, The enzyme forms dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-32 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.534, 47.414, 56.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclease


Mass: 12001.333 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 32 %
Preparation: SAD phase problem was solved with the data collected at 1.9 A wavelength, while the presented structure is refined against the 0.9184 A dataset
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.2 M ammonium sulphate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.9,0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: 2 MIRROR AND DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.91
20.91841
ReflectionResolution: 1.6→47.41 Å / Num. obs: 10804 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 13 Å2
Details: SAD phase problem was solved with the data collected at 1.9 A wavelength, while the presented structure is refined against the 0.9184 A dataset
CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Net I/σ(I): 29.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.116 / Num. unique obs: 448 / Rpim(I) all: 0.079 / Rrim(I) all: 0.142 / % possible all: 77.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
XDSdata processing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→36.28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.104
Stereochemistry target values: CCP4 geometric library, version 4.11
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 492 4.6 %RANDOM
Rwork0.188 ---
obs0.1921 10766 89.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 52.61 Å2 / Biso mean: 17.7017 Å2 / Biso min: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0 Å2
2--0.78 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 15 139 992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019957
X-RAY DIFFRACTIONr_bond_other_d00.02855
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9681302
X-RAY DIFFRACTIONr_angle_other_deg3.78231979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77821.06447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65315160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7771515
X-RAY DIFFRACTIONr_chiral_restr0.1080.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021106
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02229
X-RAY DIFFRACTIONr_mcbond_it1.3371.498468
X-RAY DIFFRACTIONr_mcbond_other1.3041.492467
X-RAY DIFFRACTIONr_mcangle_it1.9472.236594
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 33 -
Rwork0.193 661 -
all-694 -
obs--78.51 %

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