+Open data
-Basic information
Entry | Database: PDB / ID: 3zd8 | ||||||
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Title | Potassium bound structure of E. coli ExoIX in P1 | ||||||
Components | PROTEIN XNI | ||||||
Keywords | HYDROLASE / FLAP 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 / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
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. | ||||||
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 | 3zd8.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zd8.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zd8_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 3zd8_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 3zd8_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3zd8_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zd8 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zd8 | HTTPS FTP |
-Related structure data
Related structure data | 3zd9C 3zdaC 3zdbC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28203.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: XL1 BLUE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PCI857 References: UniProt: Q8X6R9, Hydrolases; Acting on ester bonds #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 53 % Description: STRUCTURE SOLVED USING MERCURY SULPHATE AND GOLD CYANIDE DERIVATIVES COLLECTED IN HOUSE |
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Crystal grow | pH: 6.5 Details: 0.2 M SODIUM THIOCYANATE, 20% PEG 3350, 0.1 M MES AT PH 6.5 |
-Data collection
Diffraction | Mean temperature: 298 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.870, 1.542, 1.542 | |||||||||
Detector | Type: ADSC QUANTUM Q4 / Detector: CCD | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. obs: 34557 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8 | |||||||||
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.1 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 2→18.22 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.292 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.169 / 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: 32.815 Å2
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Refinement step | Cycle: LAST / Resolution: 2→18.22 Å
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Refine LS restraints |
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