+Open data
-Basic information
Entry | Database: PDB / ID: 4fzx | ||||||
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Title | Exonuclease X in complex with 3' overhanging duplex DNA | ||||||
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 / SAD / Resolution: 2.3 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 | 4fzx.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fzx.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 4fzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fzx_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 4fzx_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 4fzx_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 4fzx_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/4fzx ftp://data.pdbj.org/pub/pdb/validation_reports/fz/4fzx | HTTPS FTP |
-Related 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: 5258.407 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 5156.363 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 20487.262 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 #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: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, 0.2M NaCl, 20% PEG3350, pH 8.5, 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: 0.9789 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→80 Å / Num. all: 19579 / Num. obs: 19579 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.134 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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