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- PDB-4hsb: S. pombe 3-methyladenine DNA glycosylase-like protein Mag2 bound ... -

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Basic information

Entry
Database: PDB / ID: 4hsb
TitleS. pombe 3-methyladenine DNA glycosylase-like protein Mag2 bound to damaged DNA
Components
  • DNA (5'-D(P*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3')
  • Probable DNA-3-methyladenine glycosylase 2
KeywordsHydrolase/DNA / Helix-hairpin-Helix / Non-specific DNA-binding motif / Hydrolase-DNA complex
Function / homology
Function and homology information


alkylated DNA binding / DNA-(abasic site) binding / base-excision repair, AP site formation / catalytic activity / protein-DNA complex / DNA binding / nucleus / cytoplasm
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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Alkylbase DNA glycosidase-like protein mag2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAdhikary, S. / Eichman, B.F.
CitationJournal: Dna Repair / Year: 2013
Title: Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe.
Authors: Adhikary, S. / Cato, M.C. / McGary, K.L. / Rokas, A. / Eichman, B.F.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Other
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Probable DNA-3-methyladenine glycosylase 2
B: DNA (5'-D(P*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3')
C: DNA (5'-D(P*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4155
Polymers31,2023
Non-polymers2122
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-15 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.891, 54.891, 153.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Probable DNA-3-methyladenine glycosylase 2 / 3-methyladenine DNA glycosidase 2 / 3MEA DNA glycosylase 2


Mass: 24627.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: SPBC23G7.11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O94468, DNA-3-methyladenine glycosylase II
#2: DNA chain DNA (5'-D(P*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3')


Mass: 3290.137 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*C)-3')


Mass: 3285.148 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM HEPES, 200 mM KCl, 25 mM MgSO4 , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 23, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→51.152 Å / Num. all: 22239 / Num. obs: 22239 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rsym value: 0.07 / Net I/σ(I): 30.3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
MD2data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.855 Å / SU ML: 0.16 / σ(F): 1.38 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 1121 5.05 %
Rwork0.1916 --
obs0.1937 22187 99.77 %
all-22187 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 441 14 114 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072157
X-RAY DIFFRACTIONf_angle_d1.1173000
X-RAY DIFFRACTIONf_dihedral_angle_d21.017848
X-RAY DIFFRACTIONf_chiral_restr0.07338
X-RAY DIFFRACTIONf_plane_restr0.005303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8911-1.97720.23181400.1962542X-RAY DIFFRACTION99
1.9772-2.08140.2341560.17952569X-RAY DIFFRACTION100
2.0814-2.21170.22231310.16792606X-RAY DIFFRACTION100
2.2117-2.38250.22881380.17142618X-RAY DIFFRACTION100
2.3825-2.62210.221320.1762614X-RAY DIFFRACTION100
2.6221-3.00120.24881590.18972610X-RAY DIFFRACTION100
3.0012-3.780.24911330.19542683X-RAY DIFFRACTION100
3.78-29.85840.22841320.20792824X-RAY DIFFRACTION99
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)
11.633-0.217-0.39092.1868-0.64264.4852-0.03-0.28610.16220.5433-0.00140.2906-0.3427-0.13860.0230.22580.00410.04470.1609-0.06420.205513.0583-2.1592.5761
22.77830.0839-1.66292.4775-0.01362.7235-0.04160.12770.0451-0.289-0.0601-0.18120.01110.23660.08360.15140.00010.00850.17290.030.133622.4815-6.38-20.8299
32.30080.6041-0.64876.2949-0.05332.2138-0.0516-0.1767-0.21890.24740.03580.21550.2333-0.16380.01050.17010.00580.05780.14820.02150.14512.5378-14.74510.0779
46.5067-1.5443.56181.5273-0.26012.23810.87640.4305-1.37410.8626-0.3237-0.42181.28691.1163-0.52641.83570.262-0.33782.34320.57311.091335.618-26.3944-6.7014
58.54430.11190.21633.28421.89192.6541-0.05680.044-1.45630.25530.0298-0.4111.55320.6341-0.15090.65620.17730.14530.31120.06130.422320.9359-22.8054-21.4294
62.86131.45454.60432.02422.49828.67180.3755-0.5875-1.19030.7383-0.40690.65631.435-0.66230.08880.8210.21360.31360.69040.21760.823422.7932-29.2648-18.591
72.6122.04093.01834.781-1.07957.2248-0.5223-1.8049-0.27992.0264-0.0772-0.8892-0.56790.08590.47171.04360.5071-0.18621.43120.36240.680634.8507-17.5864-7.3516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 209 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 6 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 12 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 6 )
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 12 )

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