+Open data
-Basic information
Entry | Database: PDB / ID: 3zde | ||||||
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Title | Potassium free structure of E. coli ExoIX | ||||||
Components | PROTEIN XNI | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / DNA BINDING | ||||||
Function / homology | Function and homology information DNA replication, Okazaki fragment processing / 5'-flap endonuclease activity / potassium ion binding / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 3zde.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zde.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zde_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 3zde_full_validation.pdf.gz | 426.8 KB | Display | |
Data in XML | 3zde_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 3zde_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zde ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zde | HTTPS FTP |
-Related structure data
Related structure data | 3zd8C 3zd9C 3zdaC 3zdbC 3zdcC 3zddC 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: 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: PJONEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): PCI857 References: UniProt: Q8X6R9, Hydrolases; Acting on ester bonds |
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#2: 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M SODIUM ACETATE TRIHYDRATE, 20% PEG 3350, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→40 Å / Num. obs: 9692 / % possible obs: 92.4 % / Observed criterion σ(I): 6 / Redundancy: 1.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.4 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EXOIX P21 STRUCTURE Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.887 / SU B: 9.435 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.657 / ESU R Free: 0.34 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.536 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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