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Yorodumi- PDB-3zdb: Structure of E. coli ExoIX in complex with the palindromic 5ov4 D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zdb | ||||||
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Title | Structure of E. coli ExoIX in complex with the palindromic 5ov4 DNA oligonucleotide, di-magnesium and potassium | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / FLAP ENDONUCLEASE / DNA BINDING | ||||||
Function / homology | Function and homology information DNA replication, Okazaki fragment processing / 5'-flap endonuclease activity / 5'-3' exonuclease activity / potassium ion binding / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Hemsworth, G.R. / Anstey-Gilbert, C.S. / Flemming, C.S. / Hodskinson, M.R.G. / Zhang, J. / Sedelnikova, S.E. / Stillman, T.J. / Sayers, J.R. / Artymiuk, P.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases Authors: Anstey-Gilbert, C.S. / Hemsworth, G.R. / Flemming, C.S. / Hodskinson, M.R.G. / Zhang, J. / Sedelnikova, S.E. / Stillman, T.J. / Sayers, J.R. / Artymiuk, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zdb.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zdb.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zdb_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 3zdb_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 3zdb_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3zdb_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zdb ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdb | HTTPS FTP |
-Related structure data
Related structure data | 3zd8C 3zd9C 3zdaC 3zdcC 3zddC 3zdeC 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
-Protein / DNA chain , 2 types, 2 molecules AX
#1: Protein | Mass: 28203.158 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: XL1 BLUE / Plasmid: PCI857 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8X6R9, Hydrolases; Acting on ester bonds |
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#2: DNA chain | Mass: 3680.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 208 molecules
#3: Chemical | ChemComp-K / | ||||
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#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | OLIGO DESIGNED BASED ON INITIAL STRUCTURE WITH FRAGMENT OF LARGER DNA |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M MAGNESIUM ACETATE, 15% (W/V) PEG-3350, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2009 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→33.67 Å / Num. obs: 60541 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EXOIX FLAP1 FRAGMENT COMPLEX STRUCTURE Resolution: 1.47→33.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.037 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 22.735 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→33.67 Å
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Refine LS restraints |
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