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- PDB-3oh9: AlkA Undamaged DNA Complex: Interrogation of a T:A base pair -

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Basic information

Entry
Database: PDB / ID: 3oh9
TitleAlkA Undamaged DNA Complex: Interrogation of a T:A base pair
Components
  • 5'-D(*AP*CP*AP*(BRU)P*GP*AP*AP*(BRU)P*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*AP*TP*TP*CP*AP*TP*GP*T)-3'
  • DNA-3-methyladenine glycosylase 2
KeywordsHYDROLASE/DNA / helix-hairpin-helix / DNA repair / glycosylase / alkylation / 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-5-methylcytosine 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 ...alkylated DNA binding / alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-5-methylcytosine 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 / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsBowman, B.R. / Lee, S. / Wang, S. / Verdine, G.L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of Escherichia coli AlkA in Complex with Undamaged DNA.
Authors: Bowman, B.R. / Lee, S. / Wang, S. / Verdine, G.L.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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_dif.details

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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: 5'-D(*GP*GP*CP*AP*TP*TP*CP*AP*TP*GP*T)-3'
C: 5'-D(*AP*CP*AP*(BRU)P*GP*AP*AP*(BRU)P*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)38,9213
Polymers38,9213
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-6 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.900, 139.900, 91.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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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: 32084.951 Da / Num. of mol.: 1 / Mutation: Y239C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aidA, alkA, b2068, JW2053 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RD2
References: UniProt: P04395, DNA-3-methyladenine glycosylase II
#2: DNA chain 5'-D(*GP*GP*CP*AP*TP*TP*CP*AP*TP*GP*T)-3'


Mass: 3364.208 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*CP*AP*(BRU)P*GP*AP*AP*(BRU)P*GP*CP*C)-3'


Mass: 3471.952 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25-29% peg3350, 100mM bistris, 200mM Li2SO4, 3% 6-aminocaproic acid, pH 6.0-6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2009
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19529 / Observed criterion σ(I): 19529 / Biso Wilson estimate: 54.06 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DIZ

1diz


Resolution: 2.802→41.375 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8103 / SU ML: 2.89 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 974 4.99 %
Rwork0.2047 --
obs0.2073 19529 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.979 Å2 / ksol: 0.292 e/Å3
Displacement parametersBiso max: 185.92 Å2 / Biso mean: 67.4133 Å2 / Biso min: 27.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.6909 Å20 Å20 Å2
2--1.6909 Å2-0 Å2
3----3.3819 Å2
Refinement stepCycle: LAST / Resolution: 2.802→41.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 445 0 1 2700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072815
X-RAY DIFFRACTIONf_angle_d1.0473924
X-RAY DIFFRACTIONf_chiral_restr0.061425
X-RAY DIFFRACTIONf_plane_restr0.005432
X-RAY DIFFRACTIONf_dihedral_angle_d23.1351043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8022-2.94990.33371400.26852362250283
2.9499-3.13470.31921080.27332648275690
3.1347-3.37660.33891590.2392674283394
3.3766-3.71620.28411230.22922722284595
3.7162-4.25350.21611500.17422729287995
4.2535-5.35710.20341360.16562740287695
5.3571-41.37910.23281580.18352680283893

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