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- PDB-1rrs: MutY adenine glycosylase in complex with DNA containing an abasic site -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rrs | ||||||
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Title | MutY adenine glycosylase in complex with DNA containing an abasic site | ||||||
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![]() | HYDROLASE/DNA / DNA repair / DNA glycosylase / 8-oxoguanine / protein-DNA complex / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() adenine glycosylase / adenine/guanine mispair binding / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fromme, J.C. / Banerjee, A. / Huang, S.J. / Verdine, G.L. | ||||||
![]() | ![]() Title: Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase Authors: Fromme, J.C. / Banerjee, A. / Huang, S.J. / Verdine, G.L. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN DEPOSITED IN ANY REFERENCE SEQUENCE DATABASE. ...SEQUENCE THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN DEPOSITED IN ANY REFERENCE SEQUENCE DATABASE. AUTHORS INFORMED THAT THE FOLLOWING MUTATIONS ARE PRESENT IN THE SEQUENCE: D144N, F347S, K357E. RESIDUES -2 TO 0 ARE CLONING ARTIFACTS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.4 KB | Display | ![]() |
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PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.2 KB | Display | ![]() |
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Full document | ![]() | 472.3 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rrqC ![]() 1vrlC ![]() 1munS 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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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3423.249 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3209.088 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 42091.914 Da / Num. of mol.: 1 / Mutation: D144N, F347S, K357E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: muty / Plasmid: pET28 / Production host: ![]() ![]() References: UniProt: P83847, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-Non-polymers , 3 types, 97 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-SF4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.13 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris, PEG 8000, calcium acetate, 2-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 27, 2003 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 18685 / Num. obs: 18581 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.7 / % possible all: 97.7 |
Reflection | *PLUS % possible obs: 99.4 % |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.33 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MUN Resolution: 2.4→36.58 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 523197.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.07 Å2 / ksol: 0.364404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→36.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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