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- PDB-3cwt: Crystal Structure of an AlkA Host/Guest Complex 2'-fluoro-2'-deox... -

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Basic information

Entry
Database: PDB / ID: 3cwt
TitleCrystal Structure of an AlkA Host/Guest Complex 2'-fluoro-2'-deoxyinosine:Adenine Base Pair
Components
  • DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(2FI)P*DTP*DGP*DCP*DC)-3')
  • DNA (5'-D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')
  • DNA-3-methyladenine glycosylase 2
Keywordshydrolase/DNA / AlkA / 2'-fluoro-2'-deoxyinosine / 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: 2.3 Å
AuthorsBowman, B.R. / Lee, S. / Wang, S. / Verdine, G.L.
CitationJournal: Structure / Year: 2008
Title: Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA.
Authors: Bowman, B.R. / Lee, S. / Wang, S. / Verdine, G.L.
History
DepositionApr 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 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 / struct_ref_seq / struct_site
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.db_align_beg / _struct_ref_seq.db_align_end / _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
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: DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(2FI)P*DTP*DGP*DCP*DC)-3')
F: DNA (5'-D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')
G: DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(2FI)P*DTP*DGP*DCP*DC)-3')
H: DNA (5'-D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)140,4078
Polymers140,4078
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-59 kcal/mol
Surface area54350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.748, 101.478, 103.113
Angle α, β, γ (deg.)90.00, 93.72, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a protein monomer

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Components

#1: Protein
DNA-3-methyladenine glycosylase 2 / 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 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04395, DNA-3-methyladenine glycosylase II
#2: DNA chain DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(2FI)P*DTP*DGP*DCP*DC)-3')


Mass: 3690.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 2'-fluoro-2'-deoxyinosine containing DNA
#3: DNA chain DNA (5'-D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 295 K / Method: hanging drop vapor diffusion / pH: 8
Details: PEG4000, NaCl, Na-HEPES, MgCl2, ethylene glycol, pH 8.0, hanging drop vapor diffusion, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2NaCl11
3Na-HEPES11
4MgCl211
5ethylene glycol11
6PEG400012
7NaCl12
8Na-HEPES12
9MgCl212
10ethylene glycol12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.979
2
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 88120 / % possible obs: 96.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.045 / Χ2: 1.308 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.182.70.29287470.88596.6
2.18-2.262.80.23989830.91998.5
2.26-2.372.80.17889350.98998.4
2.37-2.492.80.13189271.0398.2
2.49-2.652.80.09789251.14197.9
2.65-2.852.80.07488311.25397.4
2.85-3.142.80.05888561.5197
3.14-3.592.80.04587921.94496.4
3.59-4.522.80.03287421.80995.3
4.52-502.80.02883821.57590.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.3→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.28 3309 4.8 %
Rwork0.239 --
obs-64478 93.2 %
Solvent computationBsol: 37.089 Å2
Displacement parametersBiso mean: 49.679 Å2
Baniso -1Baniso -2Baniso -3
1--0.737 Å20 Å2-8.166 Å2
2---5.281 Å20 Å2
3---6.018 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8850 976 0 124 9950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.3371.5
X-RAY DIFFRACTIONc_scbond_it14.3022
X-RAY DIFFRACTIONc_mcangle_it5.3952
X-RAY DIFFRACTIONc_scangle_it14.4362.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3fimp.par
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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