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- PDB-3uby: Crystal structure of human alklyadenine DNA glycosylase in a lowe... -

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Basic information

Entry
Database: PDB / ID: 3uby
TitleCrystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA
Components
  • DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
  • DNA-3-methyladenine glycosylase
KeywordsHYDROLASE/DNA / alkyladenine DNA glycosylase fold / AAG / DNA repair / DNA binding / Nucleus / HYDROLASE-DNA complex
Function / homology
Function and homology information


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 / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair ...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 / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair / mitochondrial nucleoid / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / base-excision repair / damaged DNA binding / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
3-methyladenine DNA Glycosylase; Chain A / Methylpurine-DNA glycosylase (MPG) / Methylpurine-DNA glycosylase / Methylpurine-DNA glycosylase superfamily / Methylpurine-DNA glycosylase (MPG) / Formyl transferase-like, C-terminal domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-3-methyladenine glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSetser, J.W. / Lingaraju, G.M. / Davis, C.A. / Samson, L.D. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2012
Title: Searching for DNA lesions: structural evidence for lower- and higher-affinity DNA binding conformations of human alkyladenine DNA glycosylase.
Authors: Setser, J.W. / Lingaraju, G.M. / Davis, C.A. / Samson, L.D. / Drennan, C.L.
History
DepositionOct 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jan 18, 2012Group: Atomic model
Revision 1.3Jan 25, 2012Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-3-methyladenine glycosylase
B: DNA-3-methyladenine glycosylase
C: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
D: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)56,5634
Polymers56,5634
Non-polymers00
Water4,504250
1
B: DNA-3-methyladenine glycosylase

A: DNA-3-methyladenine glycosylase
C: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
D: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)56,5634
Polymers56,5634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_655y+1,-x,z+1/41
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-12 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.168, 41.168, 262.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein DNA-3-methyladenine glycosylase / 3-alkyladenine DNA glycosylase / 3-methyladenine DNA glycosidase / ADPG / N-methylpurine-DNA glycosylase


Mass: 24314.891 Da / Num. of mol.: 2 / Fragment: DELTA79AAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPG, AAG, ANPG, MID1 / Production host: Escherichia coli (E. coli)
References: UniProt: P29372, DNA-3-methyladenine glycosylase II
#2: DNA chain DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')


Mass: 3966.594 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.97 Å3/Da / Density % sol: 37.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 ...Details: An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. Crystals were obtained upon mixing 1 uL of protein-DNA complex and 1 uL of reservoir solution (100 mM BIS-TRIS, pH 5.5, 200 mM cesium chloride and 20% polyethylene glycol (PEG) 3350) over 0.5 ml of reservoir solution. Crystals appeared after incubation for 14 days at 22 degrees C, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2006
RadiationMonochromator: Double Crystal, Double Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2→66 Å / Num. all: 26998 / Num. obs: 26998 / % possible obs: 100 %
Reflection shellResolution: 2→2.053 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BNK

1bnk


Resolution: 2→65.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.087 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26545 1375 5.1 %RANDOM
Rwork0.2194 ---
obs0.22176 25556 92.12 %-
all-26998 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 354 0 250 3571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223429
X-RAY DIFFRACTIONr_angle_refined_deg1.1042.1124709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0555376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09622.029138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59915504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4941538
X-RAY DIFFRACTIONr_chiral_restr0.0680.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212502
X-RAY DIFFRACTIONr_mcbond_it2.611.51900
X-RAY DIFFRACTIONr_mcangle_it3.49923031
X-RAY DIFFRACTIONr_scbond_it5.2631529
X-RAY DIFFRACTIONr_scangle_it6.6844.51678
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 99 -
Rwork0.219 1833 -
obs--89.49 %
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)
11.8175-0.756-0.85651.830.66592.51510.04440.0808-0.07850.1421-0.10460.0499-0.07960.06030.06020.22030.0217-0.01210.0209-0.02250.12673.6984-5.009521.4544
21.7615-0.8740.80173.1614-0.66373.6281-0.06570.1840.0425-0.10140.1151-0.02690.0369-0.1413-0.04930.10010.02750.02680.1592-0.04740.1279-15.1881-26.4475-1.8766
30.54370.99391.2021.82012.22022.8380.0469-0.07520.01190.1083-0.11090.03430.10710.11850.06410.4785-0.0197-0.0250.47730.00840.2187.73561.804740.2028
41.84670.513-2.374910.8793-2.169212.92830.0918-0.52750.3550.11860.4908-0.4344-0.34250.3405-0.58260.2237-0.0591-0.02670.2337-0.13810.17119.58819.363138.6698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 200
2X-RAY DIFFRACTION1A209 - 264
3X-RAY DIFFRACTION1A268 - 290
4X-RAY DIFFRACTION2B80 - 130
5X-RAY DIFFRACTION2B144 - 160
6X-RAY DIFFRACTION2B166 - 198
7X-RAY DIFFRACTION2B208 - 262
8X-RAY DIFFRACTION2B274 - 289
9X-RAY DIFFRACTION3C1 - 11
10X-RAY DIFFRACTION4D1 - 8

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