[English] 日本語
Yorodumi- PDB-6fke: Structure of 3' phosphatase NExo (D146N) from Neisseria bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fke | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of 3' phosphatase NExo (D146N) from Neisseria bound to product DNA hairpin | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / 3' phosphatase / base excision DNA repair. | ||||||
Function / homology | Function and homology information double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / endonuclease activity / DNA repair / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis MC58 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å | ||||||
Authors | Silhan, J. / Zhao, Q. / Boura, E. / Thomson, H. / Foster, A. / Tang, C.M. / Freemont, P.S. / Baldwin, G.S. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis. Authors: Silhan, J. / Zhao, Q. / Boura, E. / Thomson, H. / Forster, A. / Tang, C.M. / Freemont, P.S. / Baldwin, G.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fke.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fke.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fke_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6fke_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 6fke_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6fke_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fke ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fke | HTTPS FTP |
-Related structure data
Related structure data | 6fk4C 6fk5C 2jc4S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29317.445 Da / Num. of mol.: 1 / Mutation: D146N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: xthA, NMB0399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K100, exodeoxyribonuclease III | ||
---|---|---|---|
#2: DNA chain | Mass: 4658.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | ChemComp-MPD / ( | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.07 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 100 mM imidazole pH = 6.6, 55 mM (NH4)2SO4, 10% (w/v) PEG 8000, 16 - 19 % (v/v) MPD, MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→54.53 Å / Num. obs: 35624 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.241 / Net I/σ(I): 2.34 |
Reflection shell | Resolution: 2.02→2.08 Å / Rmerge(I) obs: 0.5079 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JC4 Resolution: 2.151→40.075 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.63 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.151→40.075 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|