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- PDB-6fbu: Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei... -

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Basic information

Entry
Database: PDB / ID: 6fbu
TitleCrystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
Components
  • DNA (5'-D(P*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3')
  • Endonuclease 8
KeywordsHYDROLASE / Endonuclease-VIII / Nei / DNA Repair Enzyme / Covalent Intermediate
Function / homology
Function and homology information


oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Endonuclease VIII / Nei, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain ...Endonuclease VIII / Nei, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Endonuclease 8
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPomyalov, S. / Lansky, S. / Golan, G. / Zharkov, D.O. / Grollman, A.P. / Shoham, G.
CitationJournal: To Be Published
Title: Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
Authors: Pomyalov, S. / Lansky, S. / Golan, G. / Zharkov, D.O. / Grollman, A.P. / Shoham, G.
History
DepositionDec 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease 8
B: DNA (5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3')
C: DNA (5'-D(P*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0498
Polymers37,6363
Non-polymers4135
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-54 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.340, 75.340, 164.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-590-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endonuclease 8 / DNA glycosylase/AP lyase Nei / DNA-(apurinic or apyrimidinic site) lyase Nei / Endonuclease VIII


Mass: 29814.010 Da / Num. of mol.: 1 / Mutation: E2Q, P34T, T112R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nei, b0714, JW0704 / Production host: Escherichia coli (E. coli)
References: UniProt: P50465, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3')


Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')


Mass: 3863.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 210 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.8M ammonium sulfate, 0.1M sodium acetate pH / PH range: 4.6-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.102 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2→20.73 Å / Num. obs: 32845 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Rrim(I) all: 0.116 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2385 / CC1/2: 0.803 / Rpim(I) all: 0.347 / Rrim(I) all: 0.866 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
iMOSFLMdata reduction
Aimlessdata scaling
pointless1.10.25data scaling
Coot0.8.2model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OQ4

2oq4


Resolution: 2→20.251 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.06
RfactorNum. reflection% reflection
Rfree0.281 1999 6.1 %
Rwork0.2409 --
obs0.2434 32770 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 2→20.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 502 20 212 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092692
X-RAY DIFFRACTIONf_angle_d1.0653743
X-RAY DIFFRACTIONf_dihedral_angle_d14.0281997
X-RAY DIFFRACTIONf_chiral_restr0.355416
X-RAY DIFFRACTIONf_plane_restr0.006400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31431400.28042159X-RAY DIFFRACTION100
2.05-2.10530.28331410.27482167X-RAY DIFFRACTION100
2.1053-2.16720.29371380.25232140X-RAY DIFFRACTION100
2.1672-2.23710.30611410.25622153X-RAY DIFFRACTION100
2.2371-2.31690.3111420.25242180X-RAY DIFFRACTION100
2.3169-2.40960.30931390.2662157X-RAY DIFFRACTION100
2.4096-2.5190.34811430.28132186X-RAY DIFFRACTION100
2.519-2.65160.32071410.27122175X-RAY DIFFRACTION100
2.6516-2.81730.33571430.26852182X-RAY DIFFRACTION100
2.8173-3.03420.31411420.26782194X-RAY DIFFRACTION100
3.0342-3.33830.33241440.25972209X-RAY DIFFRACTION100
3.3383-3.81850.26991430.22042233X-RAY DIFFRACTION100
3.8185-4.80030.2451480.21142264X-RAY DIFFRACTION100
4.8003-20.25230.22551540.21782372X-RAY DIFFRACTION99

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