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- PDB-6fk5: Structure of 3' phosphatase NExo (D146N) from Neisseria bound to ... -

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Basic information

Entry
Database: PDB / ID: 6fk5
TitleStructure of 3' phosphatase NExo (D146N) from Neisseria bound to DNA substrate in presence of magnesium ion
Components
  • DNA (5'-D(P*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')
  • NExo D146N
KeywordsDNA BINDING PROTEIN / 3' phosphatase / base excision DNA repair / Mg2+
Function / homology
Function and homology information


: / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 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 / Exodeoxyribonuclease III
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
other sequences (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NExo D146N
B: DNA (5'-D(P*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0745
Polymers34,9072
Non-polymers1673
Water2,774154
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-28 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.940, 58.940, 292.260
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-541-

HOH

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Components

#1: Protein NExo D146N


Mass: 29317.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A8F5K9, UniProt: Q9K100*PLUS
#2: DNA chain DNA (5'-D(P*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')


Mass: 5589.642 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 3' Phosphate at the last residue / Source: (gene. exp.) other sequences (unknown) / Production host: synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.64 Å3/Da / Density % sol: 66.17 %
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, 2 mM MgCl2

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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→50.43 Å / Num. obs: 35871 / % possible obs: 99 % / Redundancy: 2 % / Rmerge(I) obs: 0.0411 / Rrim(I) all: 0.05812 / Net I/σ(I): 7.4
Reflection shellResolution: 2.02→2.08 Å / Rmerge(I) obs: 0.3141 / Rrim(I) all: 0.4442

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC4

2jc4


Resolution: 2.02→50.43 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.06
RfactorNum. reflection% reflection
Rfree0.2575 1780 4.99 %
Rwork0.2303 --
obs0.2316 35681 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→50.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 273 10 154 2498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052429
X-RAY DIFFRACTIONf_angle_d0.8743363
X-RAY DIFFRACTIONf_dihedral_angle_d18.3231392
X-RAY DIFFRACTIONf_chiral_restr0.069368
X-RAY DIFFRACTIONf_plane_restr0.005388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0061-2.06030.39921250.37832522X-RAY DIFFRACTION98
2.0603-2.1210.32321330.3452532X-RAY DIFFRACTION99
2.121-2.18940.33021340.3252574X-RAY DIFFRACTION99
2.1894-2.26770.30921390.32092512X-RAY DIFFRACTION98
2.2677-2.35850.32231360.30432555X-RAY DIFFRACTION99
2.3585-2.46580.31081260.30122570X-RAY DIFFRACTION100
2.4658-2.59580.28751210.29292577X-RAY DIFFRACTION100
2.5958-2.75840.31231370.29012585X-RAY DIFFRACTION99
2.7584-2.97140.28661530.27742588X-RAY DIFFRACTION100
2.9714-3.27040.3161350.25732651X-RAY DIFFRACTION100
3.2704-3.74350.24371400.21552633X-RAY DIFFRACTION100
3.7435-4.7160.22131560.17712691X-RAY DIFFRACTION100
4.716-54.68150.19161450.16922911X-RAY DIFFRACTION100

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