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Open data
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Basic information
Entry | Database: PDB / ID: 3u6d | ||||||
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Title | MutM set 1 GpGo | ||||||
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![]() | HYDROLASE/DNA / DNA glycosylase / DNA repair / lesion recognition / sequence context / disulfide crosslinking / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L. | ||||||
![]() | ![]() Title: Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM. Authors: Sung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.8 KB | Display | ![]() |
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PDB format | ![]() | 116 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3u6cC ![]() 3u6eC ![]() 3u6lC ![]() 3u6mC ![]() 3u6oC ![]() 3u6pC ![]() 3u6qC ![]() 3u6sC C: citing same article ( |
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Similar 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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Details | biological unit is same as asymmetric unit. |
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Components
#1: Protein | Mass: 30580.330 Da / Num. of mol.: 1 / Mutation: E3Q, Q166C,V222P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P84131, DNA-formamidopyrimidine glycosylase |
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#2: DNA chain | Mass: 4908.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA |
#3: DNA chain | Mass: 4965.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8K, sodium cacodylate, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→32.685 Å / Num. obs: 38874 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.922 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.87→32.685 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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