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Open data
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Basic information
Entry | Database: PDB / ID: 2f5o | ||||||
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Title | MutM crosslinked to undamaged DNA sampling G:C base pair IC3 | ||||||
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![]() | hydrolase/DNA / disulfide crosslink / DNA glycosylase / DNA repair / damage search / 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 | ![]() ![]() ![]() | ||||||
![]() | Banerjee, A. / Santos, W.L. / Verdine, G.L. | ||||||
![]() | ![]() Title: Structure of a DNA glycosylase searching for lesions. Authors: Banerjee, A. / Santos, W.L. / 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 | ![]() | 84.9 KB | Display | ![]() |
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PDB format | ![]() | 59.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.7 KB | Display | ![]() |
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Full document | ![]() | 466.6 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f5nC ![]() 2f5pC ![]() 2f5qC ![]() 2f5sC ![]() 1r2yS 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: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA |
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#2: DNA chain | Mass: 4850.141 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: synthetic DNA with a backbone modification containiing a dsulfide linker |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 30714.521 Da / Num. of mol.: 1 / Mutation: Q166C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: Pet24b / Production host: ![]() ![]() References: UniProt: P84131, DNA-formamidopyrimidine glycosylase |
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-Non-polymers , 3 types, 144 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 77K, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 26907 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.514 / Num. unique all: 2544 / % possible all: 89.4 |
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Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1R2Y Resolution: 2.05→42.63 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 101313.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.9074 Å2 / ksol: 0.354177 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→42.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.14 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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