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Open data
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Basic information
Entry | Database: PDB / ID: 3oh6 | ||||||
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Title | AlkA Undamaged DNA Complex: Interrogation of a C:G base pair | ||||||
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![]() | HYDROLASE/DNA / helix-hairpin-helix / DNA repair / alkylation / glycosylase / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bowman, B.R. / Lee, S. / Wang, S. / Verdine, G.L. | ||||||
![]() | ![]() Title: Structure of Escherichia coli AlkA in Complex with Undamaged DNA. Authors: Bowman, B.R. / Lee, S. / Wang, S. / Verdine, G.L. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.1 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.2 KB | Display | ![]() |
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Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ogdC ![]() 3oh9C ![]() 1dizS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32084.951 Da / Num. of mol.: 1 / Mutation: Y239C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P04395, DNA-3-methyladenine glycosylase II |
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#2: DNA chain | Mass: 3324.184 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3801.158 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.65 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.894→50 Å / Num. obs: 10809 / % possible obs: 99.8 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.106 / Χ2: 2.284 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DIZ Resolution: 2.894→35.998 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7753 / SU ML: 0.3 / σ(F): 0.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.681 Å2 / ksol: 0.282 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.53 Å2 / Biso mean: 87.6069 Å2 / Biso min: 41.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.894→35.998 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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