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- PDB-1bnk: HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA -

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Basic information

Entry
Database: PDB / ID: 1bnk
TitleHUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA
Components
  • DNA (5'-D(*GP*AP*CP*AP*TP*GP*YRRP*TP*TP*GP*CP*CP*T)-3')
  • DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')
  • PROTEIN (3-METHYLADENINE DNA GLYCOSYLASE)
KeywordsHYDROLASE/DNA / DNA REPAIR / 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 / MAD / Resolution: 2.7 Å
AuthorsLau, A.Y. / Schaerer, O.D. / Samson, L. / Verdine, G.L. / Ellenberger, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.
Authors: Lau, A.Y. / Scharer, O.D. / Samson, L. / Verdine, G.L. / Ellenberger, T.
History
DepositionJul 29, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DNA (5'-D(*GP*AP*CP*AP*TP*GP*YRRP*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: PROTEIN (3-METHYLADENINE DNA GLYCOSYLASE)


Theoretical massNumber of molelcules
Total (without water)31,8603
Polymers31,8603
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.750, 57.100, 128.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*AP*CP*AP*TP*GP*YRRP*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 PROTEIN (3-METHYLADENINE DNA GLYCOSYLASE) / E.C.3.2.2.21 / AAG / ANPG / MPG


Mass: 24051.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PLM1-AAG / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): AAG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P29372, DNA-3-methyladenine glycosylase II
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.49 Å3/Da / Density % sol: 56 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 mMprotein1drop
2100 mM1dropNaCl
320 mMHEPES1drop
40.1 mMEDTA1drop
55 %glycerol1drop
61-5 mMdithiothreitol1drop
7200 mMmagnesium acetate1reservoir
8150 mMsodium cacodylate1reservoir
90-3 mMbeta-mercaptoethanol1reservoir
1013-15 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.5418, 1.0100, 0.9787, 0.9784, 0.9500
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.011
30.97871
40.97841
50.951
ReflectionResolution: 2.7→30 Å / Num. obs: 9321 / % possible obs: 100 % / Redundancy: 9 % / Rsym value: 0.046 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 9 % / Mean I/σ(I) obs: 10 / Rsym value: 0.145 / % possible all: 100
Reflection
*PLUS
% possible obs: 99.6 % / Num. measured all: 269241 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 12.2

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Processing

Software
NameVersionClassification
MLPHAREphasing
SHARPphasing
CNS0.3Crefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→8 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.26 518 10 %RANDOM
Rwork0.216 ---
obs0.216 8482 51.7 %-
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 517 0 41 2105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.302 54
Rwork0.265 642
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / Rfactor Rwork: 0.265

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