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Open data
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Basic information
Entry | Database: PDB / ID: 1mun | ||||||
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Title | CATALYTIC DOMAIN OF MUTY FROM ESCHERICHIA COLI D138N MUTANT | ||||||
![]() | ADENINE GLYCOSYLASE | ||||||
![]() | DNA REPAIR / DNA G.A MISMATCH REPAIR ENZYME / GLYCOSIDASE / HYDROLASE | ||||||
Function / homology | ![]() adenine glycosylase / adenine/guanine mispair binding / purine-specific mismatch base pair 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 / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guan, Y. / Tainer, J.A. | ||||||
![]() | ![]() Title: MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Authors: Guan, Y. / Manuel, R.C. / Arvai, A.S. / Parikh, S.S. / Mol, C.D. / Miller, J.H. / Lloyd, S. / Tainer, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.3 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25048.004 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: D138N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P17802, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||||
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#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 65781 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.053 |
Reflection shell | Highest resolution: 1.2 Å |
Reflection | *PLUS Num. measured all: 137211 / Rmerge(I) obs: 0.053 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NATIVE MUTY Resolution: 1.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Num. disordered residues: 8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.124 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |