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Open data
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Basic information
Entry | Database: PDB / ID: 1l2b | ||||||
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Title | MutM (Fpg) DNA End-Product Structure | ||||||
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![]() | HYDROLASE/DNA / DNA Repair / DNA glycosylase / zinc finger / 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 | ![]() ![]() ![]() | ||||||
![]() | Fromme, J.C. / Verdine, G.L. | ||||||
![]() | ![]() Title: Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM. Authors: Fromme, J.C. / 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 | ![]() | 82.5 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1l1tSC ![]() 1l1zC ![]() 1l2cC ![]() 1l2dC S: Starting model for refinement 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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Unit cell |
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Components
-DNA chain , 3 types, 3 molecules BCD
#1: DNA chain | Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2482.572 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 2073.386 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 30739.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mutM / Production host: ![]() ![]() |
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-Non-polymers , 2 types, 124 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 57.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, magnesium acetate, cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 15473 / Num. obs: 12648 / % possible obs: 84.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.9 / % possible all: 82.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.101 |
Reflection shell | *PLUS % possible obs: 82.5 % / Rmerge(I) obs: 0.445 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1l1t Resolution: 2.4→50 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 41.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Total num. of bins used: 10
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor obs: 0.209 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.209 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.274 / % reflection Rfree: 10 % / Rfactor Rwork: 0.224 / Rfactor obs: 0.224 |