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- PDB-3ogd: AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair -

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Basic information

Entry
Database: PDB / ID: 3ogd
TitleAlkA Undamaged DNA Complex: Interrogation of a G*:C base pair
Components
  • 5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3'
  • 5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*G)-3'
  • DNA-3-methyladenine glycosylase 2
KeywordsHYDROLASE/DNA / helix-hairpin-helix / DNA repair / 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-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 / Hypothetical protein; 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 / DNA glycosylase / Endonuclease III; domain 1 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA-3-methyladenine glycosylase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 16, 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*CP*AP*GP*TP*CP*AP*TP*G)-3'
C: 5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)37,7363
Polymers37,7363
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-7 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.700, 139.700, 95.300
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: 32134.967 Da / Num. of mol.: 1 / Mutation: L125C
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*CP*AP*GP*TP*CP*AP*TP*G)-3'


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3'


Mass: 2845.539 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25-29% peg3350, 100mM Bis-Tris 6.0-6.6, 200mM LiSo, 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: Nov 25, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.779→50 Å / Num. obs: 12042 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.072 / Χ2: 1.349 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.980.60311880.927100
2.9-3.0280.40511790.916100
3.02-3.1580.28512041.064100
3.15-3.327.90.18211771.354100
3.32-3.537.90.13511951.642100
3.53-3.87.80.10912011.817100
3.8-4.187.50.08511951.947100
4.18-4.797.20.07112241.77399.9
4.79-6.037.10.06412261.33499.8
6.03-506.70.04512530.70995.7

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Processing

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

1diz


Resolution: 2.8→44.177 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7759 / SU ML: 2.58 / σ(F): 0.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 1043 4.88 %
Rwork0.2152 --
obs0.2179 -94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.543 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 207 Å2 / Biso mean: 102.6048 Å2 / Biso min: 60.54 Å2
Baniso -1Baniso -2Baniso -3
1--13.7597 Å2-0 Å20 Å2
2---13.7597 Å2-0 Å2
3---27.5194 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 363 0 0 2621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062728
X-RAY DIFFRACTIONf_angle_d1.0173789
X-RAY DIFFRACTIONf_chiral_restr0.059408
X-RAY DIFFRACTIONf_plane_restr0.004429
X-RAY DIFFRACTIONf_dihedral_angle_d20.9541003
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 (%)
2.779-2.92540.41131050.30842490259580
2.9254-3.10870.30041310.26392778290990
3.1087-3.34860.2571610.24572918307995
3.3486-3.68550.28371540.23223030318498
3.6855-4.21840.23481640.19933076324099
4.2184-5.31330.27191730.179830393212100
5.3133-44.18260.26111550.20643017317297

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