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- PDB-6ejv: Nuclease NucB from Bacillus licheniformis in sulphate free conditions -

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Basic information

Entry
Database: PDB / ID: 6ejv
TitleNuclease NucB from Bacillus licheniformis in sulphate free conditions
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStransky, J. / Dohnalek, J. / Oestergaard, L.A.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European Regional Development FundCZ.1.05.11.00/02.0109 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 1.1Nov 6, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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

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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)24,1253
Polymers24,0032
Non-polymers1221
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The enzyme forms dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint0 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.440, 58.470, 72.450
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.: 2
Source method: isolated from a genetically manipulated source
Details: putative EC3.1.21.1 / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: nucB, BL00126 / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q65J43
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M 1,6-Hexanediol 0.12 M 1-Butanol 0.12 M 1,2-Propanediol 0.12 M 2-Propanol 0.12 M 1,4-Butanediol 0.12 M 1,3-Propanediol 0.1 M Tris and Bicine pH 8.5 12.5 % v/v 2-Methyl- -2,4,- ...Details: 0.12 M 1,6-Hexanediol 0.12 M 1-Butanol 0.12 M 1,2-Propanediol 0.12 M 2-Propanol 0.12 M 1,4-Butanediol 0.12 M 1,3-Propanediol 0.1 M Tris and Bicine pH 8.5 12.5 % v/v 2-Methyl- -2,4,-pentanediol 12.5 % PEG 1000 12.5 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 5, 2017 / Details: HELIOS MX
RadiationMonochromator: GOEBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.75→45.5 Å / Num. obs: 24852 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 14.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.045 / Rrim(I) all: 0.101 / Net I/σ(I): 17.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1354 / CC1/2: 0.78 / Rpim(I) all: 0.518 / Rrim(I) all: 1.018 / % possible all: 100

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Processing

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

6ejs


Resolution: 1.75→45.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1667 1199 4.8 %RANDOM
Rwork0.1569 ---
obs0.1574 24802 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.45 Å2 / Biso mean: 22.3148 Å2 / Biso min: 11.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å2-0 Å2
2---0.42 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 8 280 1964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191807
X-RAY DIFFRACTIONr_bond_other_d00.021640
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9512450
X-RAY DIFFRACTIONr_angle_other_deg3.69133805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12521.95487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36715299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2551523
X-RAY DIFFRACTIONr_chiral_restr0.1140.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212091
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02416
X-RAY DIFFRACTIONr_mcbond_it1.731.759907
X-RAY DIFFRACTIONr_mcbond_other1.7191.753905
X-RAY DIFFRACTIONr_mcangle_it2.5272.6221139
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 92 -
Rwork0.243 1705 -
all-1797 -
obs--100 %

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