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- PDB-3d4v: Crystal Structure of an AlkA Host/Guest Complex N7MethylGuanine:C... -

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Basic information

Entry
Database: PDB / ID: 3d4v
TitleCrystal Structure of an AlkA Host/Guest Complex N7MethylGuanine:Cytosine Base Pair
Components
  • 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3'
  • 5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3'
  • DNA-3-methyladenine glycosylase 2
KeywordsHYDROLASE/DNA / AlkA / N7MethylGuanine / DNA repair / host-guest complex / DNA structure / DNA damage / Hydrolase / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


alkylated DNA binding / 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 / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex ...alkylated DNA binding / 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 / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex / base-excision repair / DNA repair / DNA damage response / cytoplasm
Similarity search - Function
DNA-3-methyladenine glycosylase AlkA, N-terminal / AlkA N-terminal domain / AlkA N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / : / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 ...DNA-3-methyladenine glycosylase AlkA, N-terminal / AlkA N-terminal domain / AlkA N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / : / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-3-methyladenine glycosylase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsLee, S. / Bowman, B.R. / Wang, S. / Verdine, G.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine.
Authors: Lee, S. / Bowman, B.R. / Ueno, Y. / Wang, S. / Verdine, G.L.
History
DepositionMay 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: DNA-3-methyladenine glycosylase 2
B: DNA-3-methyladenine glycosylase 2
C: DNA-3-methyladenine glycosylase 2
D: DNA-3-methyladenine glycosylase 2
E: 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3'
F: 5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3'
G: 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3'
H: 5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)140,4198
Polymers140,4198
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.100, 100.361, 102.281
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA-3-methyladenine glycosylase 2 / E.C.3.2.2.21 / DNA-3-methyladenine glycosylase II / 3-methyladenine-DNA glycosylase II / inducible / TAG II / DNA- ...DNA-3-methyladenine glycosylase II / 3-methyladenine-DNA glycosylase II / inducible / TAG II / DNA-3-methyladenine glycosidase II


Mass: 31425.236 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: alkA, aidA, b2068, JW2053 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04395, DNA-3-methyladenine glycosylase II
#2: DNA chain 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3'


Mass: 3720.442 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3'


Mass: 3638.379 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, NaCl, Na-HEPES, MgCl2, ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2NaCl11
3Na-HEPES11
4MgCl211
5ethylene glycol11
6H2O11
7PEG400012
8NaCl12
9Na-HEPES12
10MgCl212
11ethylene glycol12
12H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 32304 / % possible obs: 98.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.102 / Χ2: 1.39 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-33.60.38728900.67688.4
3-3.123.80.31731420.71896
3.12-3.2740.25432580.81299.7
3.27-3.444.10.18632711.013100
3.44-3.654.20.15532981.307100
3.65-3.944.10.13132401.636100
3.94-4.334.10.09833041.85599.9
4.33-4.9640.08532741.997100
4.96-6.244.20.07833151.624100
6.24-504.10.05333121.97898.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.9→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.275 1502 4.5 %
Rwork0.208 --
obs-30435 91.5 %
Solvent computationBsol: 22.028 Å2
Displacement parametersBiso mean: 62.049 Å2
Baniso -1Baniso -2Baniso -3
1--20.329 Å20 Å2-20.039 Å2
2--1.143 Å20 Å2
3---19.185 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8850 976 0 21 9847
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.37
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION4n7hopeedit2.par
X-RAY DIFFRACTION5CNS_TOPPAR:ion.param

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