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- PDB-8th9: Structure of mammalian NEIL2 from Monodelphis domestica in comple... -

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Basic information

Entry
Database: PDB / ID: 8th9
TitleStructure of mammalian NEIL2 from Monodelphis domestica in complex with THF-containing DNA
Components
  • DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE / NEIL2 / DNA glycosylase / DNA lyase
Function / homology
Function and homology information


DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / mitotic spindle / microtubule binding / damaged DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Formamidopyrimidine-DNA glycosylase H2TH domain / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Ribosomal protein S13-like, H2TH
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-(apurinic or apyrimidinic site) lyase
Similarity search - Component
Biological speciesMonodelphis domestica (gray short-tailed opossum)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.08 Å
AuthorsEckenroth, B.E. / Doublie, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA098993 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R50-CA233185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM143557 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural and biochemical insights into NEIL2's preference for abasic sites.
Authors: Eckenroth, B.E. / Bumgarner, J.D. / Matsumoto-Elliott, O. / David, S.S. / Doublie, S.
History
DepositionJul 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Dec 6, 2023Group: Database references / Category: citation
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
Revision 1.3Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) lyase
C: DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')
D: DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1325
Polymers40,9883
Non-polymers1442
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.430, 121.430, 117.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA-(apurinic or apyrimidinic site) lyase / NEIL2 DNA Glycosylase


Mass: 32864.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Gene: NEIL2 / Production host: Escherichia coli (E. coli)
References: UniProt: F7AMK3, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 2 types, 2 molecules CD

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


Mass: 4016.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA oligo / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3')


Mass: 4107.657 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic DNA oligo with the abasic site analog THF (3DR)
Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 61 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsDue to a large region of disorder, the wild type sequence: ...Due to a large region of disorder, the wild type sequence: FLLPKHLQKKVRLPKEKSDHKLETTSRLDGQEVPGSSLAIKALELGEEEKETVMPWWL is replaced with: GSGSG. WT Numbering is retained relative to the full length structure 6VJI.pdb for users of the structure. Met (or Mse 1) is removed post translationally by E. coli MAP (Methionine aminopeptidase) to produce the functional enzyme where Pro2 is the N-terminus.

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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: 2.93 Å3/Da / Density % sol: 58.09 %
Description: Data deposition includes the selenomethionine data as the refined model, phases, native data and heavy atoms barium, gold, cobalt along with low energy collection for sulfur/phosphate.
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM BisTris, 18% PEG 3350, 5% DMSO, 1 mM TCEP, 50 mM sodium acetate. Cryoprotection by increasing to 20% PEG 3350 and 12% DMSO. Complex (90 micromolar protein + 135 micromolar DNA) mixed 1: ...Details: 50 mM BisTris, 18% PEG 3350, 5% DMSO, 1 mM TCEP, 50 mM sodium acetate. Cryoprotection by increasing to 20% PEG 3350 and 12% DMSO. Complex (90 micromolar protein + 135 micromolar DNA) mixed 1:1 with reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.08→40 Å / Num. obs: 50479 / % possible obs: 100 % / Redundancy: 21.6 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.029 / Rrim(I) all: 0.136 / Net I/σ(I): 12.4
Reflection shellResolution: 2.08→2.14 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4515 / CC1/2: 0.522 / Rpim(I) all: 0.81 / Rrim(I) all: 2.82

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLM7.3.0data reduction
Aimless0.7.3data scaling
SHARP3.10.9phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.08→38.4 Å / SU ML: 0.3918 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.03
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: On complex per asymmetric unit but a domain (2-198) exists in two conformations throughout the crystal. Each conformation is refined at 0.5 occupancy. Refinement used secondary structure ...Details: On complex per asymmetric unit but a domain (2-198) exists in two conformations throughout the crystal. Each conformation is refined at 0.5 occupancy. Refinement used secondary structure restraints, mask refinement, heavy atom phase restraints and the wk1995 scattering table. Elevated RSRZ zones indicate the dynamics of the domain and clash score is artificially high as some near clashes from the domain get counted twice.
RfactorNum. reflection% reflection
Rfree0.2442 5027 9.96 %
Rwork0.2221 45452 -
obs0.2244 50479 99.93 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.26 Å2
Refinement stepCycle: LAST / Resolution: 2.08→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 538 5 59 2591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933637
X-RAY DIFFRACTIONf_angle_d1.19025046
X-RAY DIFFRACTIONf_chiral_restr0.0614552
X-RAY DIFFRACTIONf_plane_restr0.0095550
X-RAY DIFFRACTIONf_dihedral_angle_d21.40851338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.10.43021630.42241508X-RAY DIFFRACTION99.58
2.1-2.130.39111840.38831499X-RAY DIFFRACTION99.88
2.13-2.150.32941590.38481508X-RAY DIFFRACTION99.82
2.15-2.180.39981340.34581537X-RAY DIFFRACTION99.94
2.18-2.210.38711740.34741555X-RAY DIFFRACTION100
2.21-2.240.37121340.32321499X-RAY DIFFRACTION99.94
2.24-2.270.35321460.31661554X-RAY DIFFRACTION100
2.27-2.310.33731480.30511569X-RAY DIFFRACTION100
2.31-2.340.29451800.29291491X-RAY DIFFRACTION99.88
2.34-2.380.32891590.28431515X-RAY DIFFRACTION99.82
2.38-2.420.35171820.29641510X-RAY DIFFRACTION99.88
2.42-2.470.28811390.28121510X-RAY DIFFRACTION100
2.47-2.510.38841470.26621544X-RAY DIFFRACTION100
2.51-2.560.2591290.27051557X-RAY DIFFRACTION99.82
2.56-2.620.32141770.27421508X-RAY DIFFRACTION99.88
2.62-2.680.31991700.28661519X-RAY DIFFRACTION100
2.68-2.750.25251630.2491520X-RAY DIFFRACTION99.88
2.75-2.820.31931460.26191519X-RAY DIFFRACTION99.88
2.82-2.910.28362010.27311497X-RAY DIFFRACTION100
2.91-30.33132040.25231465X-RAY DIFFRACTION100
3-3.110.32072050.24641479X-RAY DIFFRACTION100
3.11-3.230.28541710.23891513X-RAY DIFFRACTION100
3.23-3.380.23141890.23691497X-RAY DIFFRACTION100
3.38-3.560.26211330.2041541X-RAY DIFFRACTION100
3.56-3.780.25152120.20261491X-RAY DIFFRACTION100
3.78-4.070.19931840.18741477X-RAY DIFFRACTION100
4.07-4.480.20862150.15321478X-RAY DIFFRACTION100
4.48-5.120.19111870.16281504X-RAY DIFFRACTION100
5.13-6.450.19861320.19841557X-RAY DIFFRACTION100
6.45-38.40.17381600.20151531X-RAY DIFFRACTION99.88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.717491752510.433918358498-0.4217066419123.829785928830.9716697919266.195910423640.1360798284720.0239641643876-0.02901165006690.0782076758248-0.09893292144423.47188275299E-50.175131501487-0.08313132763930.02174057075720.302533558225-0.1196857889140.04441754738950.4033009471050.05000138976060.33168527767104.5222867721.019442351138.07113528082
25.3582440599-0.141948010865-0.5322650155063.75610423604-0.6078620037655.06989226634-0.0102111851622-0.188641148227-0.1355000800510.125710843488-0.0642797271644-0.1853646220590.147413090514-0.08637599431820.1234686316110.382840722897-0.1869573418290.07147853889210.4411899460620.02964000866470.405180937332102.5745991213.676041974167.40415945497
33.824534962290.9871222214390.6481190625312.945077495831.605625514313.19919439102-0.5165855594870.8834918091940.0194840485579-0.4836258848650.4563631585490.2788979837860.353348808239-0.7047998529570.03053482775690.494615242433-0.3481546491290.1113695818420.9627277390760.09219517505610.51996692035386.0494851658-0.043609812550930.1273058956
48.52845662077-0.278576276689-1.655875016117.651295704211.946933904183.79518546057-0.8176166788641.338870129370.593932740774-0.1531887432281.06533753791-0.309064085267-0.6263885767720.472999149979-0.3293773309780.802850667437-0.223069754029-0.02646238124230.8506297144720.05990398867330.50114326332104.09406186314.312322926223.9418497471
57.91744582997-3.6458894755-1.339561526532.117412023580.4995794497952.956882581790.07426474887921.39964972448-0.494071683351-0.1078074565440.188736226873-1.479919350240.153219016968-0.357533922951-0.2954809536240.437792270995-0.2391834590490.1894106672860.737365606729-0.2079320153930.70046393703104.0066142438.595347816126.8486894574
68.356908206690.152012450626-5.911162820916.427500389723.615079557398.83762753529-1.16963252044-3.00297623443-2.048998710182.059693420181.3584883112-0.9999229277870.857385931680.357669667067-0.2058487474990.8729060160990.2585133744410.06657631467161.541066245870.1947395535661.75934466015116.0939947472.2056057820334.5192059416
71.414019472260.915259736873-3.267357393256.68113668681-0.1719756356488.16987390204-0.453820007190.05766612230991.089223961170.112032756911-0.127768369980.389675382381-0.2522536963450.4152729662920.5907314748110.798433754348-0.03766782355230.04174814733011.018222982370.1481183412891.0462034200291.918867292122.416754222932.1120601507
80.192099450242-0.9395330000680.2079848534035.439280680980.1760125597631.90900991408-0.01600544760560.9762630511551.89804685694-0.186879371677-0.309071007631-0.776223883109-1.43275151038-0.3741149978260.343443432331.09473804808-0.01938408208120.3713081748741.125131283380.1055679654161.7941875121297.547397319729.044034282426.9971651393
95.92873754485-0.892267468872-2.031258191254.01712836263-4.452958725127.212046996170.0198128092377-0.230453728748-0.09030180506730.539796913293-0.60004482926-1.34923533757-0.8452067682231.498769474580.5650096370150.608209960904-0.33761630977-0.03712635116181.47591602793-0.208858695711.81307198755120.008034536.6016934869726.3257274408
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 198 and altloc A)AA2 - 1981 - 124
22chain 'A' and (resid 2 through 198 and altloc B)AA2 - 1981 - 124
33chain 'A' and (resid 199 through 401 )AA199 - 327125 - 253
44chain 'C' and (resid 4 through 10 )CD4 - 10
55chain 'D' and (resid 5 through 11 )DE5 - 11
66chain 'C' and (resid 1 through 3 )CD1 - 3
77chain 'C' and (resid 11 through 13 )CD11 - 13
88chain 'D' and (resid 1 through 4 )DE1 - 4
99chain 'D' and (resid 12 through 14 )DE12 - 14

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