+Open data
-Basic information
Entry | Database: PDB / ID: 4fzy | ||||||
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Title | Exonuclease X in complex with 12bp blunt-ended dsDNA | ||||||
Components |
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Keywords | Hydrolase/DNA / Exo / DnaQ family / DEDDh / Exonuclease / Nuclease / Mismatch repair / UV repair / homologous recombination / stabilization of tandem repeat / Hydrolase-DNA complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication proofreading / mismatch repair / 3'-5' exonuclease activity / nucleic acid binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wang, T. / Sun, H. / Cheng, F. / Bi, L. / Jiang, T. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease Authors: Wang, T. / Sun, H.L. / Cheng, F. / Zhang, X.E. / Bi, L. / Jiang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fzy.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fzy.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fzy_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 4fzy_full_validation.pdf.gz | 464.1 KB | Display | |
Data in XML | 4fzy_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 4fzy_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/4fzy ftp://data.pdbj.org/pub/pdb/validation_reports/fz/4fzy | HTTPS FTP |
-Related structure data
Related structure data | 4fzxSC 4fzzC 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: DNA chain | Mass: 3717.439 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
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#2: Protein | Mass: 20065.205 Da / Num. of mol.: 2 / Fragment: UNP residues 1-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: exoX / Production host: Escherichia coli (E. coli) References: UniProt: P0AEK0, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters #3: DNA chain | | Mass: 3606.381 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: Chemical | ChemComp-NA / #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: 2.27 Å3/Da / Density % sol: 45.87 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1M MES, 17% PEG6000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 15314 / % possible obs: 99.8 % |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FZX Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / ESU R: 0.71 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.068 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.497→2.561 Å / Total num. of bins used: 20
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