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- PDB-6vji: Structure of mammalian NEIL2 from Monodelphis domestica -

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Basic information

Entry
Database: PDB / ID: 6vji
TitleStructure of mammalian NEIL2 from Monodelphis domestica
ComponentsNei like DNA glycosylase 2
KeywordsDNA BINDING PROTEIN / NEIL2 / base excision repair
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-(apurinic or apyrimidinic site) lyase
Similarity search - Component
Biological speciesMonodelphis domestica (gray short-tailed opossum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / MIR / Resolution: 2.54 Å
AuthorsEckenroth, B.E. / Doublie, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA098993 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA233185 United States
CitationJournal: Structure / Year: 2021
Title: Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments.
Authors: Eckenroth, B.E. / Cao, V.B. / Averill, A.M. / Dragon, J.A. / Doublie, S.
History
DepositionJan 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nei like DNA glycosylase 2
B: Nei like DNA glycosylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9984
Polymers78,8672
Non-polymers1312
Water1086
1
A: Nei like DNA glycosylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4992
Polymers39,4341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nei like DNA glycosylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4992
Polymers39,4341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.887, 67.887, 149.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 38 or resid 40...
21(chain B and (resid 5 through 38 or resid 40...
12(chain A and (resid 188 through 201 or (resid 202...
22(chain B and (resid 188 through 193 or (resid 194...
13(chain A and (resid 206 through 210 or (resid 211...
23(chain B and (resid 206 through 260 or (resid 261...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLUGLU(chain A and (resid 5 through 38 or resid 40...AA5 - 385 - 38
121LEULEUPROPRO(chain A and (resid 5 through 38 or resid 40...AA40 - 6540 - 65
131GLUGLUGLUGLU(chain A and (resid 5 through 38 or resid 40...AA6666
141PROPROZNZN(chain A and (resid 5 through 38 or resid 40...AA - C5 - 4015
151PROPROZNZN(chain A and (resid 5 through 38 or resid 40...AA - C5 - 4015
161PROPROZNZN(chain A and (resid 5 through 38 or resid 40...AA - C5 - 4015
171PROPROZNZN(chain A and (resid 5 through 38 or resid 40...AA - C5 - 4015
211PROPROGLUGLU(chain B and (resid 5 through 38 or resid 40...BB5 - 385 - 38
221LEULEUPHEPHE(chain B and (resid 5 through 38 or resid 40...BB40 - 6840 - 68
231LEULEULEULEU(chain B and (resid 5 through 38 or resid 40...BB6969
241PROPROZNZN(chain B and (resid 5 through 38 or resid 40...BB - D5 - 4015
251PROPROZNZN(chain B and (resid 5 through 38 or resid 40...BB - D5 - 4015
261PROPROZNZN(chain B and (resid 5 through 38 or resid 40...BB - D5 - 4015
271PROPROZNZN(chain B and (resid 5 through 38 or resid 40...BB - D5 - 4015
112CYSCYSSERSER(chain A and (resid 188 through 201 or (resid 202...AA188 - 201188 - 201
122GLUGLUGLUGLU(chain A and (resid 188 through 201 or (resid 202...AA202 - 203202 - 203
132PROPROZNZN(chain A and (resid 188 through 201 or (resid 202...AA - C5 - 4015
142PROPROZNZN(chain A and (resid 188 through 201 or (resid 202...AA - C5 - 4015
152PROPROZNZN(chain A and (resid 188 through 201 or (resid 202...AA - C5 - 4015
162PROPROZNZN(chain A and (resid 188 through 201 or (resid 202...AA - C5 - 4015
212CYSCYSVALVAL(chain B and (resid 188 through 193 or (resid 194...BB188 - 193188 - 193
222LYSLYSLYSLYS(chain B and (resid 188 through 193 or (resid 194...BB194194
232PROPROZNZN(chain B and (resid 188 through 193 or (resid 194...BB - D5 - 4015
242PROPROZNZN(chain B and (resid 188 through 193 or (resid 194...BB - D5 - 4015
252PROPROZNZN(chain B and (resid 188 through 193 or (resid 194...BB - D5 - 4015
262PROPROZNZN(chain B and (resid 188 through 193 or (resid 194...BB - D5 - 4015
113ARGARGLEULEU(chain A and (resid 206 through 210 or (resid 211...AA206 - 210206 - 210
123GLUGLUALAALA(chain A and (resid 206 through 210 or (resid 211...AA211 - 212211 - 212
133PROPROZNZN(chain A and (resid 206 through 210 or (resid 211...AA - C5 - 4015
143PROPROZNZN(chain A and (resid 206 through 210 or (resid 211...AA - C5 - 4015
153PROPROZNZN(chain A and (resid 206 through 210 or (resid 211...AA - C5 - 4015
163PROPROZNZN(chain A and (resid 206 through 210 or (resid 211...AA - C5 - 4015
213ARGARGLEULEU(chain B and (resid 206 through 260 or (resid 261...BB206 - 260206 - 260
223GLUGLUGLUGLU(chain B and (resid 206 through 260 or (resid 261...BB261261
233PROPROZNZN(chain B and (resid 206 through 260 or (resid 261...BB - D5 - 4015
243PROPROZNZN(chain B and (resid 206 through 260 or (resid 261...BB - D5 - 4015
253PROPROZNZN(chain B and (resid 206 through 260 or (resid 261...BB - D5 - 4015
263PROPROZNZN(chain B and (resid 206 through 260 or (resid 261...BB - D5 - 4015

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Nei like DNA glycosylase 2


Mass: 39433.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Gene: NEIL2 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F7AMK3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40 mM hepes pH 7.5, 50 mM sodium succinate, 1% propylene glycol, 1 mM TCEP, 14% PEG 3350 and cryoprotected with increase to 20% PEG 3350 and 30% glucose

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
31001N
41001N
61001N
21001N
51001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.281
SYNCHROTRONAPS 23-ID-B31.771
SYNCHROTRONAPS 23-ID-B40.9794
SYNCHROTRONAPS 23-ID-D60.979
SYNCHROTRONAPS 23-ID-B21.039
SYNCHROTRONAPS 23-ID-D51.033
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDJul 3, 2014mirrors
MARMOSAIC 300 mm CCD3CCDFeb 11, 2015mirrors
MARMOSAIC 300 mm CCD4CCDOct 16, 2015mirrors
DECTRIS PILATUS3 6M6PIXELJun 30, 2016mirrors
MARMOSAIC 300 mm CCD2CCDFeb 11, 2015mirrors
DECTRIS PILATUS3 6M5PIXELJun 30, 2016mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray2
4SINGLE WAVELENGTHMx-ray3
6SINGLE WAVELENGTHMx-ray4
2SINGLE WAVELENGTHMx-ray5
5SINGLE WAVELENGTHMx-ray6
Radiation wavelength
IDWavelength (Å)Relative weight
11.2811
21.7711
30.97941
40.9791
51.0391
61.0331
ReflectionResolution: 2.539→59.154 Å / Num. obs: 50608 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.039 / Rrim(I) all: 0.13 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 4

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.54-2.6893.3940.937150.4681.2133.76199.9
8.03-37.9611.10.069568170.9960.0220.07299.3

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDS2017-05-29data reduction
Aimless0.5.32data scaling
SHARPphasing
SOLOMONphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 2.54→37.96 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2749 4926 9.73 %
Rwork0.2503 45682 -
obs0.2527 50608 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.16 Å2 / Biso mean: 98.1896 Å2 / Biso min: 49.69 Å2
Refinement stepCycle: final / Resolution: 2.54→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 2 6 3805
Biso mean--121.37 84.16 -
Num. residues----508
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A965X-RAY DIFFRACTION9.034TORSIONAL
12B965X-RAY DIFFRACTION9.034TORSIONAL
21A150X-RAY DIFFRACTION9.034TORSIONAL
22B150X-RAY DIFFRACTION9.034TORSIONAL
31A976X-RAY DIFFRACTION9.034TORSIONAL
32B976X-RAY DIFFRACTION9.034TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5404-2.58420.38731640.3766230399
2.5842-2.63120.34712880.37642329100
2.6312-2.68180.45391880.38812338100
2.6818-2.73650.37822720.3782236100
2.7365-2.7960.39932440.36712276100
2.796-2.8610.33582280.36812293100
2.861-2.93250.40282560.34852292100
2.9325-3.01180.37722560.35962260100
3.0118-3.10040.37293310.33352230100
3.1004-3.20040.32292600.31372217100
3.2004-3.31470.29842520.30592264100
3.3147-3.44730.37793000.29322290100
3.4473-3.60410.31332800.2892256100
3.6041-3.7940.34551860.25362358100
3.794-4.03140.26321760.25052339100
4.0314-4.34230.21392320.22172262100
4.3423-4.77850.26882520.19792320100
4.7785-5.46820.22992160.21212296100
5.4682-6.88270.27242960.24232248100
6.8827-37.960.19822490.19682275100
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)
11.4587-0.75852.68951.1734-2.17193.9758-0.52390.0130.1969-0.0207-0.0247-0.0647-0.32660.0102-00.80250.0163-0.06890.4714-0.00380.6565-24.427873.854276.3324
20.47861.62463.4340.8074-0.45051.026-0.02610.1932-0.08510.1904-0.3504-0.0251-0.83640.7859-00.84810.04450.05180.61130.07180.7696-21.984370.529877.6199
31.62330.95481.32012.1610.8150.7666-0.36660.26130.3907-0.3299-0.03910.0145-0.07690.900500.73650.0092-0.02470.5540.11050.5836-25.057175.618563.5618
41.03560.22291.95593.1892-0.59991.3130.39860.91540.1312-0.3479-0.7865-0.07190.16151.0258-00.74490.39590.16060.98510.09260.5621-7.795651.793378.2214
50.349-0.28610.68250.0787-2.2945-0.1652-0.05280.2525-0.0135-0.28210.00980.397-0.03480.382301.41940.35630.12440.7695-0.06581.1174-14.346239.91784.7469
61.8982-0.7091.34351.2396-2.84544.2499-0.2019-0.3447-0.0163-0.1223-0.3062-0.01080.11070.3614-00.51260.11540.03720.67290.07190.6112-16.063759.2979103.9713
70.0449-0.0714-0.1983-0.087-0.25810.22170.95620.8176-0.361.8977-0.0223-1.1305-0.5628-0.303700.9040.1667-0.01310.676-0.01380.9351-26.988359.910186.7387
80.68551.1267-0.22951.16010.16730.5602-0.0123-0.2115-0.1792-0.1017-0.3209-0.5267-0.66641.2718-00.61810.0008-0.1240.96330.13520.7866-12.674761.346117.7172
91.3257-0.6292-0.8992-0.1466-0.22680.58950.0726-0.0588-0.13220.1608-0.4287-0.2126-0.70930.2385-00.61450.1270.00120.58190.06240.5333-16.46959.3857111.4967
102.7181-0.5588-0.85660.0766-1.223-3.7257-0.32940.2854-0.11221.6435-0.599-0.2803-2.06111.8261-01.64560.2349-0.14910.057-0.1120.5312-26.705284.8185101.929
111.67810.72231.65690.7375-2.02961.0477-0.27620.1731-0.30730.20570.28160.3726-0.21990.2891-01.32580.43890.15370.7271-0.03641.0649-40.729384.786895.6493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 63 )A5 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 147 )A64 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 187 )A148 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 279 )A188 - 279
5X-RAY DIFFRACTION5chain 'A' and (resid 280 through 326 )A280 - 326
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 63 )B5 - 63
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 132 )B64 - 132
8X-RAY DIFFRACTION8chain 'B' and (resid 133 through 168 )B133 - 168
9X-RAY DIFFRACTION9chain 'B' and (resid 169 through 188 )B169 - 188
10X-RAY DIFFRACTION10chain 'B' and (resid 189 through 279 )B189 - 279
11X-RAY DIFFRACTION11chain 'B' and (resid 280 through 325 )B280 - 325

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