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Open data
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Basic information
Entry | Database: PDB / ID: 6kij | ||||||||||||
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Title | Crystal structure of yedK with ssDNA containing an abasic site | ||||||||||||
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Function / homology | ![]() protein-DNA covalent cross-linking activity / : / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wang, N. / Bao, H. / Huang, H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK. Authors: Wang, N. / Bao, H. / Chen, L. / Liu, Y. / Li, Y. / Wu, B. / Huang, H. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124 KB | Display | ![]() |
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PDB format | ![]() | 92.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kbsSC ![]() 6kbuC ![]() 6kbxC ![]() 6kbzC ![]() 6kcqC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 25606.893 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: yedK, C4J69_22885, ECTO6_01993, EFV06_12905, EFV16_12155, SAMEA3472108_01185, SAMEA3752559_04370 Production host: ![]() ![]() ![]() References: UniProt: A0A2S5ZH06, UniProt: P76318*PLUS, ![]() |
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#2: DNA chain | Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-PED / |
#4: Chemical | ChemComp-GOL / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.49 % |
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Crystal grow![]() | Temperature: 293 K / Method: evaporation / Details: 0.2M Ammonium formate 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.579→30 Å / Num. obs: 30514 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.689 / Num. unique obs: 2980 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6KBS Resolution: 1.58→23.17 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→23.17 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.7151 Å / Origin y: 5.6189 Å / Origin z: 13.3573 Å
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Refinement TLS group | Selection details: ALL |