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- PDB-3s6i: Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) i... -

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Basic information

Entry
Database: PDB / ID: 3s6i
TitleSchizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.
Components
  • (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
  • (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
  • DNA-3-methyladenine glycosylase 1
KeywordsHYDROLASE/DNA / DNA Glycosylase / DNA repair / Helix-hairpin-Helix (HhH) / abasic site / tetrahydrofuran (THF) / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA-1,N6-ethenoadenine N-glycosylase activity / alkylated DNA binding / alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair ...DNA-1,N6-ethenoadenine N-glycosylase activity / alkylated DNA binding / alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex / damaged DNA binding / nucleus
Similarity search - Function
Endonuclease Iii, domain 2 - #40 / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 ...Endonuclease Iii, domain 2 - #40 / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-3-methyladenine glycosylase 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsAdhikary, S. / Eichman, B.F.
CitationJournal: Embo Rep. / Year: 2011
Title: Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.
Authors: Adhikary, S. / Eichman, B.F.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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: DNA-3-methyladenine glycosylase 1
B: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
C: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
D: DNA-3-methyladenine glycosylase 1
E: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
F: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0408
Polymers65,9946
Non-polymers462
Water2,018112
1
A: DNA-3-methyladenine glycosylase 1
B: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
C: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0204
Polymers32,9973
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-29 kcal/mol
Surface area12380 Å2
MethodPISA
2
D: DNA-3-methyladenine glycosylase 1
E: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
F: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0204
Polymers32,9973
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-31 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.317, 112.298, 61.113
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-3-methyladenine glycosylase 1 / 3-methyladenine DNA glycosidase 1 / 3MEA DNA glycosylase 1


Mass: 26423.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: mag1, SPAPB24D3.04c / Plasmid: pBG100 / Production host: Escherichia coli (E. coli) / Strain (production host): C41
References: UniProt: Q92383, DNA-3-methyladenine glycosylase II
#2: DNA chain (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')


Mass: 3191.073 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#3: DNA chain (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')


Mass: 3382.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES (pH 6.5), 20% (w/v) PEG 8K and 2.4% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM10.9792
SYNCHROTRONAPS 21-ID-D20.97872
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 16, 2009
MARMOSAIC 300 mm CCD2CCDFeb 17, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.978721
ReflectionResolution: 2.28→29.1 Å / Num. all: 32231 / Num. obs: 32231 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 40.8 Å2 / Rsym value: 0.109 / Net I/σ(I): 11.5
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3176 / Rsym value: 0.404 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.28→29.1 Å / SU ML: 0.64 / σ(F): 1.35 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1631 5.07 %random
Rwork0.1849 ---
all0.2362 32199 --
obs0.1869 32188 97.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.382 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1752 Å2-0 Å21.0957 Å2
2---2.3552 Å2-0 Å2
3---9.5304 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 845 2 112 4143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084196
X-RAY DIFFRACTIONf_angle_d1.1855864
X-RAY DIFFRACTIONf_dihedral_angle_d21.871577
X-RAY DIFFRACTIONf_chiral_restr0.068663
X-RAY DIFFRACTIONf_plane_restr0.005605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.277-2.34390.2383860.21761871X-RAY DIFFRACTION71
2.3439-2.41960.26251480.20392544X-RAY DIFFRACTION99
2.4196-2.5060.27541470.19792601X-RAY DIFFRACTION100
2.506-2.60630.23461410.2062602X-RAY DIFFRACTION100
2.6063-2.72480.26231450.20842604X-RAY DIFFRACTION100
2.7248-2.86830.24561480.21022610X-RAY DIFFRACTION100
2.8683-3.04790.26991360.19812616X-RAY DIFFRACTION100
3.0479-3.28290.20851270.19112625X-RAY DIFFRACTION100
3.2829-3.61270.24291310.16712623X-RAY DIFFRACTION100
3.6127-4.13420.18241390.15372626X-RAY DIFFRACTION100
4.1342-5.20380.17641320.1462628X-RAY DIFFRACTION100
5.2038-29.10560.20091510.16812607X-RAY DIFFRACTION98
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)
11.8103-1.09220.47042.3258-0.61990.68310.08570.3957-0.05810.006-0.0918-0.28020.09540.02270.0080.14730.02720.00310.20130.03970.2239-23.092-10.509-6.6375
20.8415-0.91990.33553.166-0.9570.976-0.08870.1582-0.2275-0.04090.30960.5915-0.0383-0.2743-0.19560.08440.01830.0330.19160.08720.2006-40.3994-8.782-4.9127
30.9105-0.5468-0.22040.9315-0.38160.5959-0.0695-0.05080.81830.1427-0.1053-0.8629-0.21740.39860.17890.10320.0098-0.10160.23620.03180.4654-16.0715-2.3271-1.2033
41.2008-1.13871.74062.93760.11962.21530.24820.11610.4417-0.5739-0.42010.2555-0.3077-0.55370.2010.23440.0438-0.07350.2977-0.01430.3117-40.6524-34.063314.6793
51.09750.1053-0.51021.73190.75981.3108-0.0811-0.03790.0728-0.06040.1157-0.178-0.03330.2315-0.06660.0635-0.0026-0.02240.176-0.04220.1046-15.4127-36.362329.3272
60.823-0.40290.63420.360.19440.8646-0.0324-0.1564-0.1139-0.0471-0.05490.4424-0.0183-0.39170.09510.1147-0.0018-0.03420.229-0.00930.2903-39.18-38.441225.9458
70.7236-0.08770.85674.8545-2.71433.1794-0.06830.15730.02951.3938-0.4766-0.5662-1.12120.27860.31730.38190.1099-0.08160.13620.04220.1137-28.526-11.65114.5949
83.073-0.86270.71683.3019-3.24110.4207-0.656-1.47750.03012.06310.2566-0.2862-0.82430.39930.35670.77230.1658-0.23220.587-0.01320.3744-29.3632-12.246914.7463
91.4719-2.1411-1.56375.61792.05611.1332-0.21930.1119-0.17851.2822-0.14670.99150.2697-0.11430.29070.37140.05310.16310.1294-0.04010.218-30.1511-32.194744.5575
100.1050.8552-0.30191.5792-0.71871.7698-0.1492-0.36220.15240.59050.12880.86750.0306-0.38840.10410.31410.17830.21850.3623-0.11730.4431-28.7828-29.866644.7184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 17:74)
2X-RAY DIFFRACTION2(chain A and resid 75:163)
3X-RAY DIFFRACTION3(chain A and resid 164:220)
4X-RAY DIFFRACTION4(chain D and resid 17:42)
5X-RAY DIFFRACTION5(chain D and resid 43:164)
6X-RAY DIFFRACTION6(chain D and resid 165:219)
7X-RAY DIFFRACTION7chain B
8X-RAY DIFFRACTION8chain C
9X-RAY DIFFRACTION9chain E
10X-RAY DIFFRACTION10chain F

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