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- PDB-6fke: Structure of 3' phosphatase NExo (D146N) from Neisseria bound to ... -

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Basic information

Entry
Database: PDB / ID: 6fke
TitleStructure of 3' phosphatase NExo (D146N) from Neisseria bound to product DNA hairpin
Components
  • DNA (5'-D(*GP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*A)-3')
  • Exodeoxyribonuclease III
KeywordsDNA BINDING PROTEIN / 3' phosphatase / base excision DNA repair.
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / endonuclease activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Exodeoxyribonuclease III-like / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily ...Exodeoxyribonuclease III-like / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Exodeoxyribonuclease III
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsSilhan, J. / Zhao, Q. / Boura, E. / Thomson, H. / Foster, A. / Tang, C.M. / Freemont, P.S. / Baldwin, G.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust084369/Z/ 07/Z United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis.
Authors: Silhan, J. / Zhao, Q. / Boura, E. / Thomson, H. / Forster, A. / Tang, C.M. / Freemont, P.S. / Baldwin, G.S.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Exodeoxyribonuclease III
B: DNA (5'-D(*GP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2045
Polymers33,9752
Non-polymers2283
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-17 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.929, 58.929, 292.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

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Components

#1: Protein Exodeoxyribonuclease III


Mass: 29317.445 Da / Num. of mol.: 1 / Mutation: D146N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: xthA, NMB0399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K100, exodeoxyribonuclease III
#2: DNA chain DNA (5'-D(*GP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*A)-3')


Mass: 4658.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.74 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 100 mM imidazole pH = 6.6, 55 mM (NH4)2SO4, 10% (w/v) PEG 8000, 16 - 19 % (v/v) MPD, MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.02→54.53 Å / Num. obs: 35624 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.241 / Net I/σ(I): 2.34
Reflection shellResolution: 2.02→2.08 Å / Rmerge(I) obs: 0.5079

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC4

2jc4


Resolution: 2.151→40.075 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 1223 4.21 %
Rwork0.2001 --
obs0.2011 29065 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→40.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 247 10 173 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012401
X-RAY DIFFRACTIONf_angle_d0.9563320
X-RAY DIFFRACTIONf_dihedral_angle_d22.264889
X-RAY DIFFRACTIONf_chiral_restr0.066362
X-RAY DIFFRACTIONf_plane_restr0.006387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1505-2.23660.35441310.32832970X-RAY DIFFRACTION98
2.2366-2.33840.32291290.29912995X-RAY DIFFRACTION98
2.3384-2.46160.32651340.27243035X-RAY DIFFRACTION99
2.4616-2.61590.23181310.23513007X-RAY DIFFRACTION99
2.6159-2.81780.21641370.22773083X-RAY DIFFRACTION99
2.8178-3.10120.22551360.23253086X-RAY DIFFRACTION100
3.1012-3.54980.25961360.20893102X-RAY DIFFRACTION100
3.5498-4.47140.2091390.17083176X-RAY DIFFRACTION100
4.4714-40.08210.17321500.15773388X-RAY DIFFRACTION99

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