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Yorodumi- PDB-2nqj: Crystal structure of Escherichia coli endonuclease IV (Endo IV) E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nqj | ||||||
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Title | Crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant bound to damaged DNA | ||||||
Components |
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Keywords | HYDROLASE / Tim_barrel / trinuclear zinc site | ||||||
Function / homology | Function and homology information deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding ...deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Garcin-Hosfield, E.D. / Hosfield, D.J. / Tainer, J.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Authors: Garcin, E.D. / Hosfield, D.J. / Desai, S.A. / Haas, B.J. / Bjoras, M. / Cunningham, R.P. / Tainer, J.A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ALTHOUGH CHAIN B COULD BE MOVED BY A SYMMETRY OPERATION, THE COMPLEX FORMED BY CHAIN B WITH CHAIN C AND D IS NOT BIOLOGICALLY RELEVANT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nqj.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nqj.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 2nqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nqj_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 2nqj_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 2nqj_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 2nqj_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/2nqj ftp://data.pdbj.org/pub/pdb/validation_reports/nq/2nqj | HTTPS FTP |
-Related structure data
Related structure data | 2nq9C 2nqhC 1qtwS 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4446.864 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 4626.984 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 31517.512 Da / Num. of mol.: 2 / Mutation: E261Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: nfo- strain BW565DE3 / Gene: nfo / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6C1, deoxyribonuclease IV #4: Chemical | ChemComp-ZN / #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: 2.45 Å3/Da / Density % sol: 49.79 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% MPEG-2000, 0.1M HEPES pH 7, 0.4M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 24943 / % possible obs: 93 % / Rsym value: 0.095 / Net I/σ(I): 14.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QTW Resolution: 2.45→20 Å / σ(F): 0
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Solvent computation | Bsol: 50.958 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.078 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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Xplor file |
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