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- PDB-5omt: Endonuclease NucB -

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Basic information

Entry
Database: PDB / ID: 5omt
TitleEndonuclease NucB
ComponentsNucB
KeywordsHYDROLASE / Endonuclease / biofilm / Bacillus subtilis / DNA
Function / homologyDeoxyribonuclease NucA/NucB / NucB
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsBasle, A. / Lewis, R.J.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Crystal structure of NucB, a biofilm-degrading endonuclease.
Authors: Basle, A. / Hewitt, L. / Koh, A. / Lamb, H.K. / Thompson, P. / Burgess, J.G. / Hall, M.J. / Hawkins, A.R. / Murray, H. / Lewis, R.J.
History
DepositionAug 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: NucB


Theoretical massNumber of molelcules
Total (without water)12,0141
Polymers12,0141
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.955, 59.955, 66.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NucB


Mass: 12014.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: nucB / Production host: Bacillus subtilis (bacteria) / References: UniProt: F1BV52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH6.5 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→44.56 Å / Num. obs: 27361 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.991 / Net I/σ(I): 16.1
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1316 / CC1/2: 0.944 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimlessdata scaling
SHELXCDphasing
SHELXEmodel building
ARP/wARPmodel building
BUCCANEERmodel building
REFMAC5.8.0158refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.35→44.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.528 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18623 1369 5 %RANDOM
Rwork0.1485 ---
obs0.15034 25934 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.443 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.79 Å20 Å2
3---1.58 Å2
Refinement stepCycle: 1 / Resolution: 1.35→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 0 104 943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019870
X-RAY DIFFRACTIONr_bond_other_d0.0020.02780
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9431178
X-RAY DIFFRACTIONr_angle_other_deg0.99631808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63422.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03415140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7841510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021005
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3021.506441
X-RAY DIFFRACTIONr_mcbond_other2.2241.494440
X-RAY DIFFRACTIONr_mcangle_it2.8122.261551
X-RAY DIFFRACTIONr_mcangle_other2.8352.27552
X-RAY DIFFRACTIONr_scbond_it3.4581.949429
X-RAY DIFFRACTIONr_scbond_other3.3431.925426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9012.757623
X-RAY DIFFRACTIONr_long_range_B_refined4.52119.4411005
X-RAY DIFFRACTIONr_long_range_B_other4.42419.011984
X-RAY DIFFRACTIONr_rigid_bond_restr2.17631650
X-RAY DIFFRACTIONr_sphericity_free18.023576
X-RAY DIFFRACTIONr_sphericity_bonded10.77451656
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 85 -
Rwork0.184 1891 -
obs--100 %

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