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Yorodumi- PDB-2nqh: High Resolution crystal structure of Escherichia coli endonucleas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nqh | ||||||
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Title | High Resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant | ||||||
Components | Endonuclease 4 | ||||||
Keywords | HYDROLASE / Tim-Barrel / trinuclear zinc center | ||||||
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: 1.1 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nqh.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nqh.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nqh_validation.pdf.gz | 429.4 KB | Display | wwPDB validaton report |
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Full document | 2nqh_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 2nqh_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 2nqh_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/2nqh ftp://data.pdbj.org/pub/pdb/validation_reports/nq/2nqh | HTTPS FTP |
-Related structure data
Related structure data | 2nq9C 2nqjC 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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Unit cell |
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-Components
#1: Protein | Mass: 31517.512 Da / Num. of mol.: 1 / Mutation: E261Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfo / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): nfo- strain BW565DE3 / References: UniProt: P0A6C1, deoxyribonuclease IV | ||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: 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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 20% MPEG-2000, 0.1M HEPES pH 5.9, 0.1mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. obs: 102718 / % possible obs: 92 % / Rsym value: 0.072 / Net I/σ(I): 19.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QTW Resolution: 1.1→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 16.723 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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