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- PDB-1f6o: CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1f6o
TitleCRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH DNA
Components
  • 3-METHYL-ADENINE DNA GLYCOSYLASE
  • DNA (5'-D(*GP*AP*CP*AP*TP*GP*(YRR)P*TP*TP*GP*CP*CP*T)-3')
  • DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')
KeywordsHYDROLASE/DNA / Protein-DNA Complex / AAG DNA repair glycosylase / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


alkylbase DNA N-glycosylase activity / DNA-3-methyladenine glycosylase II / 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 ...alkylbase DNA N-glycosylase activity / DNA-3-methyladenine glycosylase II / 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 / 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: 2.4 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
DepositionJun 22, 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 1.3Feb 7, 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_conn_type / 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_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
D: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(YRR)P*TP*TP*GP*CP*CP*T)-3')
E: DNA (5'-D(*GP*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)32,1604
Polymers32,1373
Non-polymers231
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.75, 57.10, 128.45
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*(YRR)P*TP*TP*GP*CP*CP*T)-3')


Mass: 3832.501 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein 3-METHYL-ADENINE DNA GLYCOSYLASE / E.C.3.2.2.20 / AAG / ALKYLADENINE DNA GLYCOSYLASE


Mass: 24328.916 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P29372, DNA-3-methyladenine glycosylase I
#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


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2magnesium acetate11
3sodium cacodylate11
4PEG 800012
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.3 mMprotein1
2100 mMsodium chloride1
320 mMHEPES1
40.1 mMEDTA11
55 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: PHILLIPS / Detector: CCD / Date: Jun 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→500 Å / Num. all: 13118 / Num. obs: 11332 / % possible obs: 86.4 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 21.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.253 / Num. unique all: 1643 / % possible all: 75.6
Reflection
*PLUS
Num. obs: 13252 / % possible obs: 86.1 % / Num. measured all: 100868
Reflection shell
*PLUS
% possible obs: 75.6 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→500 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: Used Powell conjugate gradient minimization and torsion angle-restrained molecular dynamics
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1166 10.3 %Random
Rwork0.219 ---
all-13118 --
obs-11332 86.4 %-
Refinement stepCycle: LAST / Resolution: 2.4→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 517 1 134 2290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2

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