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- PDB-1ewn: CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1ewn
TitleCRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH 1,N6-ETHENOADENINE-DNA
Components
  • 3-METHYL-ADENINE DNA GLYCOSYLASE
  • DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDA)P*TP*TP*GP*CP*C)-3')
  • DNA (5'-D(P*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')
Keywordshydrolase/DNA / DNA repair / glycosylase / AAG / ANPG / MPG / 3-methyladenine DNA glycosylase / 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 / DNA alkylation repair / Displacement of DNA glycosylase by APEX1 ...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 / DNA alkylation repair / Displacement of DNA glycosylase by APEX1 / 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 / 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 / Resolution: 2.1 Å
AuthorsLau, A.Y. / Wyatt, M.D. / Glassner, B.J. / Samson, L.D. / Ellenberger, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG.
Authors: Lau, A.Y. / Wyatt, M.D. / Glassner, B.J. / Samson, L.D. / Ellenberger, T.
History
DepositionApr 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDA)P*TP*TP*GP*CP*C)-3')
E: DNA (5'-D(P*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')
A: 3-METHYL-ADENINE DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6844
Polymers31,6613
Non-polymers231
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.145, 57.336, 125.517
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDA)P*TP*TP*GP*CP*C)-3')


Mass: 3686.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 1,N6-ETHENOADENINE-DNA
#2: DNA chain DNA (5'-D(P*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')


Mass: 3646.405 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein 3-METHYL-ADENINE DNA GLYCOSYLASE / E.C.3.2.2.21 / ALKYLADENINE DNA GLYCOSYLASE / AAG


Mass: 24327.932 Da / Num. of mol.: 1 / Fragment: E125Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Keywords: 2
References: UniProt: P29372, DNA-3-methyladenine glycosylase II
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl2, Tris-HCl, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HClTris11
2MgCl211
3glycerol11
4PEG 400011
5MgCl212
6glycerol12
7PEG 400012
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1200 mMmagnesium chloride1reservoir
2100 mMTris-HCl1reservoir
324 %(w/v)PEG40001reservoir
410 %glycerol1reservoir
51
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.01
DetectorType: BRANDEIS / Detector: CCD / Date: Jul 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.1→500 Å / Num. all: 18433 / Num. obs: 18163 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.201 / Num. unique all: 2183 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 247464
Reflection shell
*PLUS
% possible obs: 97.8 % / Mean I/σ(I) obs: 6.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.1→500 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: Powell conjugate gradient minimization and torsion angle-restrained molecular dynamics
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1793 9.9 %RANDOM
Rwork0.23 ---
all-18433 --
obs-18163 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 490 1 80 2109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_bond_d0.006

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