+Open data
-Basic information
Entry | Database: PDB / ID: 6kcq | ||||||||||||
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Title | Crystal structure of yedK with ssDNA containing an abasic site | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA repair / abasic site | ||||||||||||
Function / homology | Function and homology information protein-DNA covalent cross-linking activity / : / Lyases / Hydrolases; Acting on peptide bonds (peptidases) / SOS response / single-stranded DNA binding / peptidase activity / DNA damage response / proteolysis Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å | ||||||||||||
Authors | Wang, N. / Bao, H. / Huang, H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kcq.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kcq.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kcq ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kcq | HTTPS FTP |
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-Related structure data
Related structure data | 6kbsSC 6kbuC 6kbxC 6kbzC 6kijC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25738.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: yedK, C4J69_22885, ECTO6_01993, EFV06_12905, EFV16_12155, SAMEA3472108_01185, SAMEA3752559_04370 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2S5ZH06, UniProt: P76318*PLUS, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: DNA chain | Mass: 3269.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.67 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.05M calcium chloride dihydrate 0.1M Bis-Tris pH6.5 30% MPEG550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
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: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 24080 / % possible obs: 99.1 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.409 / Num. unique obs: 2271 / CC1/2: 0.444 / Rpim(I) all: 0.22 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6kbs Resolution: 1.701→37.61 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 17.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.701→37.61 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: 24.1299 Å / Origin y: 60.7069 Å / Origin z: -5.748 Å
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Refinement TLS group | Selection details: all |