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- PDB-2f5s: Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f5s | ||||||
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Title | Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC1 | ||||||
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![]() | hydrolase/DNA / disulfide crosslink / DNA glycosylase / DNA repair / damage search / control complex / 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 | ![]() | 82.8 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 451 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f5nC ![]() 2f5oC ![]() 2f5pC ![]() 2f5qC ![]() 1r2yS 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
#1: DNA chain | Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4866.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA containing a backbone modification |
#3: Protein | Mass: 30713.537 Da / Num. of mol.: 1 / Mutation: E3Q, Q166C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: Pet24b / Production host: ![]() ![]() References: UniProt: P84131, DNA-formamidopyrimidine glycosylase |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
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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 350K, 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: 2.35→50 Å / Num. obs: 17996 / % possible obs: 95 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1783 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1R2Y Resolution: 2.35→37.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 259602.7 / 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: 37.2366 Å2 / ksol: 0.339025 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→37.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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