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- PDB-3w0f: Crystal structure of mouse Endonuclease VIII-LIKE 3 (mNEIL3) -

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Basic information

Entry
Database: PDB / ID: 3w0f
TitleCrystal structure of mouse Endonuclease VIII-LIKE 3 (mNEIL3)
ComponentsEndonuclease 8-like 3
KeywordsHYDROLASE / HELIX TWO TURNS HELIX / ZINC FINGER / DNA binding
Function / homology
Function and homology information


Cleavage of the damaged purine / MCM complex binding / DNA N-glycosylase activity / bubble DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / interstrand cross-link repair / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair ...Cleavage of the damaged purine / MCM complex binding / DNA N-glycosylase activity / bubble DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / interstrand cross-link repair / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / single-stranded DNA binding / chromosome / double-stranded DNA binding / damaged DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Zinc finger GRF-type profile. / Zinc finger, GRF-type / GRF zinc finger / Zinc finger, DNA glycosylase/AP lyase-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / 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 ...Zinc finger GRF-type profile. / Zinc finger, GRF-type / GRF zinc finger / Zinc finger, DNA glycosylase/AP lyase-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / 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 / 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 / Zinc finger domain / Helicase, Ruva Protein; domain 3 - #50 / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Endonuclease 8-like 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsLiu, M. / Imamura, K. / Averill, A.M. / Wallace, S.S. / Doublie, S.
Citation
Journal: Structure / Year: 2013
Title: Structural Characterization of a Mouse Ortholog of Human NEIL3 with a Marked Preference for Single-Stranded DNA
Authors: Liu, M. / Imamura, K. / Averill, A.M. / Wallace, S.S. / Doublie, S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo
Authors: Liu, M. / Bandaru, V. / Bond, J.P. / Jaruga, P. / Zhao, X. / Christov, P.P. / Burrows, C.J. / Rizzo, C.J. / Dizdaroglu, M. / Wallace, S.S.
History
DepositionOct 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease 8-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4216
Polymers31,8481
Non-polymers5735
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.580, 43.823, 77.645
Angle α, β, γ (deg.)90.00, 128.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endonuclease 8-like 3 / DNA glycosylase FPG2 / DNA glycosylase/AP lyase Neil3 / Endonuclease VIII-like 3 / Nei-like protein 3


Mass: 31847.887 Da / Num. of mol.: 1 / Fragment: glycosylase domain, UNP residues 2-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: mouse, Neil3 / Plasmid: pETDuet2-T7EcoMap-ORF6-MmuNeil3 324 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star (DE3)
References: UniProt: Q8K203, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.4 Å3/Da / Density % sol: 48.76 % / Description: THE SF FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG 3350, 0.15M DL-malic acid, 0.1M HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONAPS 23-ID-B21.2808
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEJul 7, 2010mirror
MARMOSAIC 300 mm CCD2CCDNov 15, 2010Si(111) Double Crystal Monochrometer
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MAR MIRRORSSINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.28081
ReflectionResolution: 2→40 Å / Num. all: 40028 / Num. obs: 37958 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 16.46
Reflection shellResolution: 2→2.09 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.64 / Num. unique all: 1976 / % possible all: 97.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
CNS1.3refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→38.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 627378.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: 1. BULK SOLVENT MODEL USED. 2. THE FRIEDEL PAIRS WERE USED IN PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3669 9.7 %RANDOM
Rwork0.197 ---
all0.201 40082 --
obs0.197 37958 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.8312 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å22.8 Å2
2--4.12 Å20 Å2
3----3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 5 169 2175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 373 9.9 %
Rwork0.283 4781 -
obs-3800 75.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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