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Yorodumi- PDB-6fk5: Structure of 3' phosphatase NExo (D146N) from Neisseria bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fk5 | ||||||
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Title | Structure of 3' phosphatase NExo (D146N) from Neisseria bound to DNA substrate in presence of magnesium ion | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / 3' phosphatase / base excision DNA repair / Mg2+ | ||||||
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) other sequences (unknown) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fk5.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fk5.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fk5 ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fk5 | HTTPS FTP |
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-Related structure data
Related structure data | 6fk4C 6fkeC 2jc4S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29317.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A8F5K9, UniProt: Q9K100*PLUS | ||||
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#2: DNA chain | Mass: 5589.642 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 3' Phosphate at the last residue / Source: (gene. exp.) other sequences (unknown) / Production host: synthetic construct (others) | ||||
#3: Chemical | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.17 % |
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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, 2 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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→50.43 Å / Num. obs: 35871 / % possible obs: 99 % / Redundancy: 2 % / Rmerge(I) obs: 0.0411 / Rrim(I) all: 0.05812 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.02→2.08 Å / Rmerge(I) obs: 0.3141 / Rrim(I) all: 0.4442 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JC4 Resolution: 2.02→50.43 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→50.43 Å
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Refine LS restraints |
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LS refinement shell |
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